Mass spectrometer system

ABSTRACT

During the structural analysis of a protein or peptide by tandem mass spectroscopy, a peptide ion derived from a protein that has already been measured and that is expressed in great quantities is avoided as a tandem mass spectroscopy target. A peptide derived from a minute amount of protein, which has heretofore been difficult to analyze, can be automatically determined as a tandem mass spectroscopy target within the real time of measurement. Data concerning a protein that has already been measured and a peptide derived from the protein is automatically stored in an internal database. The stored data is collated with measured data with high accuracy to determine an isotope peak. In this way, the process of selecting a peptide peak that has not been measured as the target for the next tandem analysis can be performed within the real time of measurement and a redundant measurement of peptides derived from the same protein can be avoided. The information contained in the MS n  spectrum is effectively utilized in each step of the MS n  involving a multi-stage dissociation and mass spectroscopy (MS n ), so that the flows for the determination of the next analysis content and the selection of the parent ion for the MS n+1  analysis, for example, can be optimized within the real time of measurement and with high efficiency and accuracy. Thus, a target of concern to the user can be subjected to tandem mass spectroscopy without wasteful measurement.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a mass spectroscopy spectrum analysissystem using a mass spectrometer, and to a system for automaticallydetermining an optimum flow of mass spectroscopy within a measurementtime in order to identify the chemical structure of biopolymers, such aspolypeptides or sugars, with high precision and efficiency.

2. Background Art

In a general mass spectroscopy, a sample as the object of measurement isionized, and a variety of resultant ions are delivered to a massspectrometer for measuring the ion intensity for each mass-to-chargeratio m/z, which is the ratio of the mass number m of ion to the valencez. As a result, a mass spectrum is obtained, which consists of a peak ofthe measured ion intensity (ion peak) for each mass-to-charge ratio m/zvalue. Such a mass spectroscopic analysis of the ionized sample in afirst dissociation step is called MS¹. In tandem mass spectrometer, inwhich multiple-stage isolation is possible, an ion peak having aspecific mass-to-charge ratio m/z is selected (the selected ion speciesis called a parent ion) from the ion peaks detected by MS¹, and the thusselected ion is dissociated and broken up by collision with gasmolecules or the like. The resultant dissociated ion species is thensubjected to mass spectroscopy, thereby obtaining a mass spectrum in asimilar manner. The n-stage dissociation of the parent ion and thesubjecting of the dissociated ion species to mass spectroscopy arereferred to as MS^(n+1). Thus, in the tandem mass spectrometer, theparent ion is dissociated in multiple stages (1, 2, . . . , n stages),and the mass number of the ion species generated in each stage isanalyzed (MS², MS³, . . . , MS^(n+1)).

(1) Most of the mass spectrometers capable of tandem analysis areequipped with a data-dependent function whereby, when selecting theparent ion for MS² analysis from the ion peaks in MS¹, the ion peaks areselected in decreasing intensities (such as the ion peaks in the top 10strongest-intensities) as the parent ions, and then they are subjectedto dissociation and mass spectroscopy (MS²).

(2) The ion-trapping type mass spectrometer manufactured by Finningan isequipped with a Dynamic Exclusion function whereby, when selecting aparent ion for MS² analysis from the ion peaks in MS¹, the ion specieshaving a mass-to-charge ratio m/z value that is designated by the userin advance is excluded from the selection as a parent ion.

(3) Known examples relating to the determination of correspondencebetween a measured ion species and an ion species that has been measuredinclude the following:

Patent Document 1: JP Patent Publication (Kokai) No. 2001-249114 A

Patent Document 2: JP Patent Publication (Kokai) No. 10-142196 A 1998

In Patent Document 1, a characteristic peak in the first-stage spectrumdata and the spectrum data in the second stage of the corresponding ionspecies are stored in a database. In the subsequent measurements,spectrum data obtained by mass spectroscopy in the second stage of asample as the object of measurement is compared with the second-stagespectrum data in the database in order to determine the degree ofcorrespondence. Data components with the highest degree ofcorrespondence is outputted as the comparison result.

In Patent Document 2, a measurement is continuously carried out during amultiple-stage dissociation measurement without conducting a sampleinjection process during measurement so that an ion intensityfluctuation due to injection between the MS^(n) and MS^(n+1) data can beprevented. In this way, the need for the addition of a standard samplecan be eliminated, thereby enabling an efficient quantitative analysis.The routine returns to MS^(n+1) or proceeds to the next MS¹ measurement,depending on whether or not the data corresponds to the designated iondata that has been already collected in the MS^(n) and MS^(n+1) dataanalysis.

Reviews of Modern Physics, Vol. 62 (1990), pp. 531-540, provides a basicdescription of an ion trap. A cross section of a basic configuration ofthe ion trap is shown in FIG. 15. The ion trap, which is a quadrupoleion trap, is made up of two end-cap electrodes and a single ringelectrode. An RF voltage is applied to these electrodes such that aquadrupole electric field is formed at the center of these electrodes,thus enabling the trapping of gaseous ions three dimensionally. Bycontinuously varying the RF voltage, the mass of the ions that aredischarged can be controlled. A quadrupole pole is made up of fourparallel poles. By applying a RF voltage to the electrodes, gaseous ionscan be two dimensionally trapped at the center of the electrodes. Bycontrolling the RF voltage that is applied, it becomes possible todischarge ions with a specific mass or, conversely, trap only those ionswith a specific mass.

A tandem mass spectroscopy (MS/MS) can be conducted using a quadrupoleion trap, as described in the U.S. Pat. No. Re. 34000. In thisapparatus, those ions for which no analysis is required are dischargedprior to MS/MS. Namely, the removal of the ions for which no analysis isrequired is not conducted prior to the primary mass spectroscopy. A RFvoltage that resonates with the ions is then applied in order toincrease the kinetic energy. As a result of these operations,dissociated ions (fragment ions) are created by the collision induceddissociation (CID) with remaining molecules. By subjecting thesefragment ions to mass spectroscopy (tandem mass spectroscopy), the massof the fragment ions can be determined. In this case, it is necessary toinitially conduct a mass spectroscopy without involving a CID (primarymass spectroscopy) in order to determine the ions as the object of atandem mass spectroscopy (MS/MS, or a secondary mass spectroscopy). Itis also possible to repeat a similar operation to further conduct atandem mass spectroscopy (MSn) on a specific dissociated ion.

Recently, mass spectroscopic methods are often employed for anexhaustive analysis of proteins. Analytical Chemistry, Vol. 73 (2001),pp.5683-5690, describes examples of analysis called a shotgun analysis.In this technique, a peptide mixture prepared by subjection a protein toenzymatic digestion is separated using a liquid chromatograph, and aseparated sample is then subjected to a tandem mass spectroscopy using aquadrupole ion-trap mass spectrometer. With reference to the determinedmass of the ion and that of the fragment ion, a database of proteins orgenes is searched in order to identify a protein. In case the types ofthe peptide mixture are too numerous, each peptide might not becompletely separated in the liquid chromatograph, and a plurality ofkinds of peptides might be simultaneously introduced into the massspectrometer. This gives rise to the need for automatic tandem analysiscalled data-dependent analysis. Specifically, the band width of aseparated sample separated in a liquid chromatograph is in the order ofone minute, and the number of kinds of ions that can be subjected totandem mass spectrometer at one time is limited to five. In many cases,the ions with greater ion intensities are preferentially subjected totandem mass spectroscopy, although this depends on the setting of thedata-dependent analysis.

A technical material for the quadrupole ion-trap mass spectrometermanufactured by ThermoFinnigan(www.thermo.com/eThermo/CMA/PDFs/Articles/articlesFile_(—)10918.pdf)describes a dynamic exclusion function. Prior to the start of analysis,the masses of those ions to be excluded from tandem mass analysis areentered and then a list is prepared. By this operation, it becomespossible to exclude those ions put on the list as the objects ofdata-dependent analysis (tandem mass spectrometer). When this functionis to be employed, a conventional mass spectroscopy is conducted firstwithout involving the CID, and then the mass of the ions to be detectedis determined. Next, priorities of the ions as the objects of tandemmass spectroscopy are determined in the detected ions, whereupon thoseions put on the list are excluded from the objects of data-dependentanalysis (tandem mass spectroscopy).

SUMMARY OF THE INVENTION

(1) With the data-dependent function referred to in (1) of theBackground of Art section, as proteins that are expressed in greatquantities or peptides derived from proteins are preferentiallysubjected to tandem analysis, the possibility is very high that proteinsor peptides that have already been identified are redundantly measured,which would lead to a waste of measurement time and the sample. Althoughthe focus of analysis has so far been centered on those proteins thatare expressed in great amounts, it is expected that the focus will shifttoward the analysis of minute quantities of proteins such as pathologicproteins in the future. With the data-dependent function, it isdifficult to perform tandem analysis of minute amounts of proteins indetail.

(2) According to the dynamic exclusion function referred to in (2) ofthe Background Art section, it is determined whether or not an ionspecies has the mass-to-charge ratio m/z value designated by the user inadvance on the basis of the mass-to-charge ratio m/z value. Thus, thereis the possibility that the ion species with different mass number m orvalence z but with the same the mass-to-charge ratio m/z value aresimilarly excluded from the targets of the MS² analysis.

In order to avoid this problem, it is necessary to make thedetermination as to whether or not an ion species is that which has beendesignated in advance based on the valence z and mass number m of eachion peak, rather than on the mass-to-charge ratio m/z value, althoughthe mass-to-charge ratio m/z value of each ion peak is apparent from themass spectrum. In this determination, it is necessary to calculate thevalence z and mass number m of each ion peak on a real-time basis duringmeasurement.

In Patent Documents 1 and 2, for the MS^(n) data analysis, theidentification of a specific ion species is conducted by referring to adatabase, for example. In Patent Documents 1 and 2 too, the registeredvalues in the database are mass-to-charge ratio m/z values, and the massnumber m is not necessarily employed. Alternatively, monovalent ions(z=1) have been presumed. Information obtained from the MS analysisother than the measurement values of the mass-to-charge ratio m/z (suchas the characteristic data for each of the valence z and mass number m)is not utilized either. Thus, it cannot be said that appropriateinformation has been utilized for an efficient selection of ions.

(3) When the number of amino acid residues constituting a peptide chainis K and the number of kinds of amino acids is 20, the number ofpossible amino acid sequences is as many as 20^(K). Add to this thechemical modifications to the amino acid side chains, and the numberbecomes much larger. Further, as the number of amino acid residuesincreases, so does the number of the isotopes of the peptide chains. Inparticular, while the intensity of the isotope peaks decreases withregard to small peptide chains, the intensity of the isotope peaksactually becomes stronger in the case of large peptide chains. If theisotope peaks are set as the parent ion species for the subsequentdissociation measurement, the accuracy of search and collation in aprotein database that is eventually conducted drops significantly, somuch so that, for large peptides, data processing might becomedifficult.

In order to solve the aforementioned problem, it is necessary toeffectively utilize the information contained in the MS^(n) spectrum ineach stage of MS^(n), and to perform the selection of the parent ion forthe determination of the subsequent analysis content and for theMS^(n+1) analysis within the real-time of measurement efficiently andaccurately.

Moreover, of the mixture samples that are simultaneously introduced intothe mass spectrometer, the number of those samples that can be subjectedto tandem mass spectroscopy is limited. In particular, since there aremuch impurity components in the aforementioned shot gun analysis, forexample, there are many cases in which ions exist that have such a lowion intensity that a tandem mass spectroscopy cannot be conductedthereon, which leads to the problem that the tandem mass spectroscopycannot be conducted on a minute amount of a sample that needs analysis.This is due to the fact that even with the data-dependent analysis, ionswith greater ion intensities are preferentially subjected to tandem massspectroscopy such that only those ions that are not the objects ofanalysis can possibly be analyzed. The aforementioned dynamic exclusionmethod is effective only in cases where the substances that do not needanalysis are known in advance. In cases where unknown impuritycomponents are present in great quantities, it might be impossible toconduct a tandem mass spectroscopy on a minute amount of a sample thatneeds analysis.

In view of the foregoing, it is an object of the invention to provide atandem mass spectroscopy employing a mechanism for selecting ananalysis-target ion and, optionally, a non-analysis target ion, prior tothe primary mass spectroscopy, so that a minute amount of a sample thatneeds analysis can be analyzed even in cases where unknown impuritycomponents are present in great quantities.

In order to solve the aforementioned problems (1) to (3) in a massspectrometer capable of tandem analysis, the invention provides a systemin which mainly the below-indicated means (1) to (5) are adopted. Inthis system, a target ion is subjected to dissociation n−1 times andthen to mass spectroscopy, and the resultant mass spectrum (MS^(n)) issubjected to fast analysis within the real-time of measurement in orderto determine the subsequent analysis content.

(1) It is determined, at a high speed, whether or not each ion peak inthe mass spectrum (MS^(n)) is an isotope peak.

(2) If the ion peak is determined to be an isotope peak, the valence zand mass number m of the ion peak are calculated from the interval 1/zof the isotope peaks, and it is then determined, based on the massnumber m, whether or not the ion peak corresponds to the ion speciesthat has been designated in advance.

(3) In cases where a liquid chromatography (LC) is installed in a stageprior to the mass spectrometer, the retention time of LC is also used asa factor in making the determination, in order to distinguish ionspecies with the same mass number m but with different structures.

(4) In order to prevent redundant measurement, data concerning the massnumbers or retention time of peptides that have already been measuredonce or of those peptides derived from proteins that have already beenidentified is stored in an internal database built inside the massspectroscopy system. It is then determined at high speed whether or notthe stored data corresponds to each ion peak in the mass spectrum(MS^(n)).

(5) During the selection of the next analysis target, isotope peaks areavoided.

The aforementioned object of the invention is achieved by the followingfeatures:

(1) Using a first database in which the data about an analysis objectcandidate substance is recorded and an RF power supply for applying anRF voltage for the elimination of an ion that is not an analysis object,an ion that is not listed in the first database and that is not ananalysis object, or a non-analysis object ion that corresponds to thedata in a second database in which data about non-analysis objectcandidate substance is recorded, is eliminated by the RF voltage priorto a primary mass spectroscopy. In this way, the adverse influence fromnon-analysis object ions can be avoided and an analysis object ion canbe detected in mass spectroscopy.

(2) Alternatively, after the primary mass spectroscopy and before thedissociation process involving collision induced dissociation (CID) withremaining molecules and the mass spectroscopy (tandem mass spectroscopy)of a dissolved ion, an analysis object ion listed in the first databasein which data about an analysis object candidate substance is recordedis selected and subjected to CID, and then tandem mass spectroscopy isperformed. As a result, an analysis object ion that exists in onlyminute amounts can be reliably subjected to tandem mass spectroscopy.

(3) The features (1) and (2) may be combined.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 schematically shows the flow of an automatic determinationprocess in the mass spectroscopy flow according to a first embodiment ofthe invention.

FIG. 2 schematically shows a mass spectroscopy system as a whole formeasuring mass spectroscopy data in the first embodiment of theinvention.

FIGS. 3A, 3B and 3C show examples of a multi-stage dissociation and massspectroscopy flow.

FIG. 4 schematically shows the content of an internal database automaticstorage process.

FIG. 5 schematically shows the internal database storage contentaccording to the invention.

FIG. 6 schematically shows the content of an isotope peak determinationprocess.

FIG. 7 schematically shows an estimated isotope listing process in theisotope peak determination process.

FIG. 8 schematically shows the process of calculation of valence andmass number in the isotope peak determination process.

FIG. 9A shows the probability of appearance of 20 types of amino acidsin a living body, and the mass number of peptide chains.

FIG. 9B shows the calculation of an isotope peak intensity distributionand the process of determining a final isotope peak in the isotope peakdetermination process of the invention.

FIG. 10 shows an example of display of the m/z, m, and z of each peakand the number of contained isotopes in the result of the isotope peakdetermination process of the invention.

FIG. 11 shows an example of the timings of carrying out the processesshown in FIGS. 1, 12, 13, 14, and 20 according to the invention withinthe real time of mass spectroscopy measurement.

FIG. 12 schematically shows an automatic determination process in themass spectroscopy flow according to a second embodiment of theinvention.

FIG. 13 schematically shows an automatic determination process in themass spectroscopy flow according to a third embodiment of the invention.

FIG. 14 schematically shows an automatic determination process in themass spectroscopy flow according to a fourth embodiment of theinvention.

FIG. 15 shows an intensity distribution pattern of isotope peaksdepending on the mass number.

FIG. 16 schematically shows the content of an isotope determinationprocess according to a fifth embodiment of the invention.

FIG. 17 schematically shows the selection of a parent ion for tandemmass spectroscopy according to a sixth embodiment of the invention.

FIG. 18 shows examples of isotope patterns of a plurality of ion specieswith identical m/z value in a seventh embodiment of the invention.

FIG. 19 shows the concept of the selection of the next tandem massspectroscopy target using isotope labeling in an eighth embodiment ofthe invention.

FIG. 20 schematically shows an automatic determination process in themass spectroscopy flow according to a ninth embodiment of the invention.

FIG. 21 shows the concept of the selection of the next tandem massspectroscopy target in a 10^(th) embodiment of the invention.

FIG. 22 schematically shows a mass spectroscopy system as a wholeaccording to an 11^(th) embodiment of the invention.

FIG. 23 schematically shows a mass spectroscopy system as a wholeaccording to a 12^(th) embodiment of the invention.

FIG. 24 schematically shows a mass spectroscopy system as a wholeaccording to a 13^(th) embodiment of the invention.

FIG. 25 schematically shows a mass spectroscopy system as a wholeaccording to a 14^(th) embodiment of the invention.

FIG. 26 schematically shows an automatic determination process in themass spectroscopy flow according to a 15^(th) embodiment of theinvention.

FIG. 27 schematically shows an internal database in the 15^(th)embodiment of the invention.

FIG. 28 shows the concept of a quality evaluation of mass spectroscopydata in the 15^(th) embodiment of the invention.

FIG. 29 shows the concept of data processing in the internal database ina 16^(th) embodiment of the invention.

FIG. 30 shows the concept of an automatic determination process in amass spectroscopy flow in the 16^(th) embodiment of the invention.

FIG. 31 shows the concept of addition of MS² data and MS^(n) (n≧3) in a17^(th) embodiment of the invention.

FIG. 32 shows the concept of addition of data using a differentdissociation method in an 18^(th) embodiment of the invention.

FIG. 33 shows the concept of changing addition process conditions for aplurality of items of mass spectrum data in a 19^(th) embodiment of theinvention.

FIG. 34 shows the concept of addition of an isotope peak intensity and amonoisotopic peak intensity in a 20^(th) embodiment of the invention.

FIG. 35A schematically shows a typical flow of protein analysis andprotein identification in the prior art.

FIG. 35B shows the concept of a flow of protein analysis and proteinidentification in a 22^(nd) embodiment of the invention.

FIG. 36 shows the flow of a system process determination in a 22^(nd)embodiment of the invention.

FIG. 37 shows an example of the result of analysis in the 22^(nd)embodiment of the invention.

FIG. 38 shows the flow of a system process determination in a 23^(rd)embodiment of the invention.

FIG. 39 shows the flow of a system process determination in a 24^(th)embodiment of the invention.

FIG. 40 shows the concept of a peak group in a 25^(th) embodiment of theinvention.

FIG. 41 shows the flow of a system process determination in a 25^(th)embodiment of the invention.

FIG. 42 shows the flow of a system process determination in a 25^(th)embodiment of the invention.

FIG. 43 shows an example of apparatus configuration in the firstembodiment of the invention.

FIG. 44 shows an example of apparatus configuration in the firstembodiment of the invention.

FIG. 45 shows an example of apparatus configuration in the firstembodiment of the invention.

FIG. 46 shows the system configuration of a mass spectroscopy systemaccording to an embodiment of the invention.

FIG. 47 shows an example of the analysis flow in a mass spectroscopysystem based on another embodiment of the invention.

FIG. 48 shows an example of the analysis flow in a mass spectroscopysystem based on another embodiment of the invention.

FIG. 49 shows an example of the analysis flow in a mass spectroscopysystem based on yet another embodiment of the invention.

FIG. 50 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention.

FIG. 51 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention employing a linear trap.

FIG. 52 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention employing a quadrupole ion trap massspectrometer.

FIG. 53 schematically shows how an ion is trapped by the ion trap.

FIG. 54 shows a diagram of a mass spectroscopy system based on anotherembodiment of the invention employing MALDI in an ion source.

FIG. 55 shows a diagram of a mass spectroscopy system based on anotherembodiment of the invention employing MALDI in an ion source.

FIG. 56 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention employing MALDI in an ion source.

FIG. 57 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention.

FIG. 58 shows a diagram of a mass spectroscopy system based on yetanother embodiment of the invention.

FIG. 59 shows an example of mass spectrum obtained by a massspectroscopy system based on yet another embodiment of the invention.

FIG. 60 shows a cross section of a quadrupole ion trap according to theprior art.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

Embodiments of the invention will be hereafter described by referring tothe drawings.

A first embodiment will be described. FIG. 1 shows a flowchart of aprocess for automatically determining the analysis content in a massspectroscopy system according to the first embodiment of the invention.Mass spectroscopy data 1 refers to the data measured in a massspectroscopy system 19 shown in FIG. 2. In the mass spectroscopy system19, a sample as the object of analysis is preprocessed in apreprocessing system 11, such as a liquid chromatography. For example,if the sample is a protein, the protein is broken up by a digestiveenzyme into the size of polypeptides, and then separated andfractionated by gas chromatography (GC) or liquid chromatography (LC) ina preprocessing system 11. In the following description of an example,LC is adopted as the separating and fractionating system in thepreprocessing system 11. After the separation and fractionation of thesample, the sample is ionized in an ionization unit 12 and is thenseparated in a mass spectroscopy unit 13 depending on the mass-to-chargeratio m/z of the ion, where m is the mass of the ion and z is the chargevalence thereof. The separated ion is detected in an ion detection unit14 and the data is then arranged and processed in a data processing unit15. The result of analysis, namely the mass spectroscopy data 1, isdisplayed by a display unit 16. The entire series of mass spectroscopyprocess—the ionization of the sample, transport and incidence of thesample ion beam onto the mass spectroscopy unit 13, the step of massseparation, ion detection, and data processing—is controlled by acontrol unit 17.

Mass spectroscopy methods can be roughly divided into those whereby asample is ionized and then analyzed as is (MS analysis methods), and thetandem mass spectroscopy methods whereby a specific sample ion (parention) is selected based on its mass, the parent ion is dissociated, andthen the resultant dissociated ion is subjected to mass spectrometer.The tandem mass spectroscopy methods also have a function for performingthe dissociation and mass spectroscopy in multiple stages (MS^(n)) suchthat ions (precursor ions) with a specific mass-to-charge ratio areselected from the dissociated ions, the precursor ions are furtherdissociated, and the resultant dissociated ions are subjected to massspectroscopy. Specifically, after measuring the mass analysisdistribution of substances in the original sample as mass spectrum data(MS¹), parent ions with a certain m/z value are selected and thendissociated. After measuring the mass spectroscopy data (MS²) of theresultant dissociated ions, the selected precursor ions are furtherdissociated, and the mass spectroscopy data (MS³) of the resultantdissociated ions is measured, thus performing the dissociation and massspectroscopy process in multiple stages (MS^(n) (n≧3)). In each stage ofdissociation, information about the molecular structure of the precursorions in a state prior to dissociation is obtained, which is very usefulin estimating the structure of the precursor ions. The more detailed thestructural information of the precursors, the higher the accuracy ofestimation becomes of the structure of the parent ion, which is theoriginal structure.

In the present embodiment, as a method of dissociating the precursorions, the collision induced dissociation method is adopted, whereby theprecursor ions are caused to collide with buffer gas, such as helium, inorder to dissociate the ions. For the collision induced dissociation, aneutral gas, such as helium gas, is required. Thus, a collision cell 13Afor collision induced dissociation may be provided separately from themass spectroscopy unit 13, as shown in FIG. 2. Alternatively, however, aneutral gas may be filled in the mass spectroscopy unit 13 so that thecollision induced dissociation can take place within the massspectroscopy unit 13. In this case, the collision cell 13A may bedispensed with. Further alternatively, the electron capture dissociationtechnique may be employed as the dissociation means, whereby low-energyelectrons are irradiated in order to allow the parent ions to capturelarge amounts of low-energy electrons so that the target ions can bedissociated.

FIG. 3A shows a conventional method of automatically determining theflow of tandem mass spectroscopy. When further selecting a target ion(parent ion) for dissociation and mass spectroscopy from the spectrum ofMS¹, which is the mass spectroscopy distribution of the substances inthe sample according to the conventional technique, ions are selected inthe order of decreasing intensities. Even during the selection ofprecursor ions in MS² and thereafter, ion peaks with higher intensitiesare similarly selected. In this type of automatic method of determiningthe flow of tandem mass spectroscopy, when the sample is a protein, forexample, peptide ions that have been enzymatically broken down fromproteins that are expressed in great quantities tend to become thetarget of tandem mass spectroscopy. As a result, it becomes more likelythat those proteins that are expressed in great quantities areexclusively analyzed in redundant manner.

Thus, in accordance with the invention, it is determined whether themass number m of all of the peptides that are expected to be producedupon enzymatic hydrolysis of predesignated proteins, or the retentiontime of LC corresponds to the value of each ion peak in the measuredMS¹. Then, based on the result of determination, the parent ion that isto become the target for the next tandem mass spectroscopy isautomatically determined on a real-time basis during measurement (suchas within 100 msec, 10 msec, 5 msec, or 1 msec). For example, a case isconsidered where a protein A that is expressed in great quantities hasalready been measured and identified, and only those minute amounts ofproteins that have not been measured are to be subjected to tandem massspectroscopy. As shown in FIG. 4, peptides that are expected to beproduced by the enzym-digestive cutting of the amino acid sequence ofprotein A, as an identified protein, that has been predesignated arelisted. At the same time, the manner of cutting of the amino acids ismodified based on the type of digestive enzyme that was entered inadvance by the user via a user input unit 18 and that was used in thepreprocessing system 11. For example, in the event that the userselected trypsin as the digestive enzyme in the preprocessing system 11,if there is arginine (R) or lysine (K) in the amino acid sequence as thecharacteristics of the cutting of the amino acid sequence of theprotein, the binding between R or K and the amino acid bound to the Cterminal thereof is cut off. In an exception, however, if proline (P) isbound to the C terminal of R or K, that binding is not cut off. Namely,as the characteristics of the peptide that is cut off, the amino acid atthe C terminal is either R or K at all times. The amino acid at the Nterminal does not become P except in cases where the amino acid at the Nterminal is P in the amino acid sequence of the original protein. Such acutting rule differs from one digestive enzyme to another. As an exampleof the digestive cutting process, a case will be considered whereprotein A is human myoglobin. In the event that human myoglobin with theamino acid sequence shown in FIG. 4 is enzymatically digested withtrypsin, the production of 22 kinds of peptides shown in FIG. 4 can beexpected based on the aforementioned cutting rule concerning trypsinenzymatic digestion. Thus, cleaved peptides in accordance with thecutting rule of digestive enzyme are derived, and the amino acidsequence and mass number are determined for each of the derived peptidesand then stored in an internal database 10. In the case where thepeptide ion derived from a protein designated by the user is the “Ionspecies designated in advance or during measurement” shown in FIG. 3B,the characteristics data concerning the peptide ion (such as the massnumber and the retention time data, if any, for LC) derived from theuser-designated protein, as described above, are already stored in theinternal database 10. Accordingly, the MS¹ data that has just beenmeasured is read at a high rate, and then the internal database 10 issearched within a preparation time (such as 100 msec, 10 msec, 5 msec,or 1 msec) before the next measurement to see if the MS¹ datacorresponds, with a certain tolerance, to the stored data in thedatabase 10. From the peaks of the ion species that do not correspond,within a certain tolerance, to the stored data in the internal database10, ions are selected in decreasing order of intensity as the parentions for MS², which is the next tandem analysis. The parent ions aredissociated to obtain dissociated ions, which are then subjected to massspectroscopy in the MS² analysis. If, for example, all of the peaks thatappeared in the MS¹ data correspond, within a certain tolerance, to thestored data in the internal database 10, it is determined that there isno appropriate peak for the parent ion for the MS² analysis, and theroutine automatically proceeds to the measurement for the MS¹ analysisinstead of the MS² analysis. Thus, in accordance with the presentembodiment, in the case where proteins that are expressed in greatquantities or proteins that have already been measured or identified aredesignated in advance, and the characteristics data (such as the massnumber and the retention time for LC) for the peptides derived fromthose proteins is stored in the internal database 10, the peptidesderived from the proteins that are expressed in large quantities can beexcluded from the targets for the next tandem analysis. Thus, thepossibility is increased that ion peaks with relatively low intensitiesbecome the target of tandem mass spectroscopy. In other words, ascompared with the conventional cases where the tandem analysis isfocused on ions with high intensities, the number of proteins that areidentified can be expected to increase in accordance with the presentembodiment.

In the above-described example, the target substance about which thecharacteristics data is stored in the internal database 10 has beenproteins that are expressed in large quantities or peptides derived fromproteins that have already been measured and identified. However, asshown in FIG. 5, it is also possible to store the characteristics dataabout the ion species (such as a peptide, a sugar chain, a peptide witha modification structure, or a chemical substance) that has been oncesubjected to the MS^(n) (n≧2) analysis in the internal database 10during measurement as needed so as to avoid an overlap of tandemanalysis on the same ion species. Moreover, in accordance with thepresent embodiment, it is also possible to store the characteristicsdata about the ion species derived from noise or impurities in theinternal database 10 so as to avoid conducting the tandem massspectroscopy (MS^(n)) on noise or impurities. The ion species derivedfrom noise or impurities may be designated by the user in advance.Alternatively, the ion species that has been determined to be noise maybe automatically stored in the internal database 10 during measurement.

Via the user input unit 18, the user can enter information indicatingwhether or not an isotope peak detection is necessary, whether or not acollation and search with reference to the internal database isnecessary, the tolerance for the determination of data correspondence inthe collation and search with reference to the internal database, andthe resolution during the selection of the parent ion, for example, inaddition to the types of digestive enzyme.

The present embodiment is also characterized in that as thecharacteristics data about the ion species that is designated either inadvance or during measurement, the mass number, rather than themass-to-charge ratio m/z, is used. When the mass-to-charge ratio m/z isutilized as the characteristics data to be checked against the storeddata in the internal database 10, those ion species with correspondingm/z values but with different mass number m or valence z are preventedfrom being selected as the target of tandem mass spectroscopy. On theother hand, by employing the mass number m as the data to be checked, asin the present embodiment, those ion species with corresponding m/zvalues but with different mass number m or valence z can be recognized,so that the targets for tandem mass spectroscopy can be more accuratelyselected. Moreover, those corresponding ion species (with the same massnumber m) with different valence z or m/z values can be recognized asthe same ion species, so that they can be prevented from being selectedas targets for tandem mass spectroscopy over and over again.Alternatively, ion species with the same mass number m and differentvalence z may be recognized as separate ion species and selected astargets for tandem mass spectroscopy.

Since there exist different ions species with the same mass number m,the data concerning the retention time of LC in the preprocessing system11 may be stored in the internal database 10 and then utilized. When thesample passes through the LC column, the equilibrium constant ofadsorption and desorption onto the LC column differs due to the chemicalcharacteristics of the substance, resulting in different lengths of time(retention time or holding time) it takes for the sample to exit thecolumn. Thus, it is possible to distinguish different species with thesame mass number m by taking advantage of the aforementioned fact, i.e.,based on the difference in the LC retention time arising from differentchemical structures or characteristics. In accordance with the presentembodiment, the determination as to whether or not a particular ionspecies is an ion species designated in advance or during measurement ismade on the basis of data capable of more accurately specifying the ionspecies, such as the mass number and the retention time of LC. Thus,only those targets that are to be subjected to tandem mass spectroscopycan be accurately analyzed, thereby enabling the user to obtain desiredanalysis data without wasteful measurement.

Hereafter, the content of the characteristics data will be described. Asshown in FIG. 5, with regard to the ion species (such as a peptide,sugar chain, a peptide with a modification structure, chemicalsubstance, and impurity-derived substance) on which analysis has beenconducted up to the MS^(n) (n≧2) analysis, the mass number m, valence z,mass-to-charge ratio m/z, the retaining time τ of LC, ion intensity, andanalysis conditions are stored as the characteristics data. In the casewhere the peak of the ion species that has been referred to whenderiving the mass number m is accompanied by an isotope peak, the massnumber m is that of the peak that does not include an isotope. Theanalysis conditions include the operation conditions concerning the massspectrometer (such as the value of the voltage applied to theelectrodes, the analysis sequence, and so on), the value of n in thetandem analysis MS^(n) (n≧2) conducted on the particular ion species,the date of measurement, and the column numbers of LC or GC used. Otherinformation that may be stored in the internal database 10 include: theratio of solvent or mobile phase of LC or GC; the flow volume orgradient of LC or GC; the number of the sample divided in the ionexchanger in a one-dimensional LC in cases where a two-dimensional LC isemployed; the spot position, number or coordinates in the sample platein cases where a MADLI ion source is employed; and the content ofmeasures taken with regard to the ion species that corresponded to thestored characteristics data (namely, whether the ion species thatcorresponded to the stored characteristics data should be avoided as atarget for the MS^(n) (n≧2) analysis, whether or not the ion speciesshould be selected in a preferential manner as a target for the MS^(n)(n≧2) analysis, or whether or not the ion species should be removed whenthe ion is injected into the mass spectroscopy system, or prior to theinjection). The content of measures taken with regard to the ion speciesthat corresponded to the stored characteristics data may alternativelybe designated by the user for each ion species. In the case where, asthe content of measures taken with regard to the ion species thatcorresponded to the stored characteristics data, the ion species isdesignated to be removed upon or prior to the injection of the sampleinto the mass spectroscopy system, if an ion reservoir portion orfunction is provided, such as an ion trap (FIG. 22 b) or a linear trap(FIG. 24 b), a measure may be taken to prevent the trapping of an ion inthe ion reservoir portion by, for example, applying an auxiliary voltagein an superposed manner in order to resonate and discharge the ion thatneeds to be removed (FIGS. 22 b or 24 b), upon injection of ions intothe ion reservoir portion. In particular, those ions for which noanalysis with very high intensity is required may be registered in theinternal database with a comment “To be removed upon or prior toinjection of the ion into the mass spectroscopy system”. In this way,the accumulation of large quantities of impurity ions can be avoided, sothat low-intensity ions can be accumulated very efficiently and can beexpected to be subjected to highly accurate analysis.

Depending on the content of measures taken on the ion species thatcorrespond to the stored characteristics data (namely, whether or notthe ion species corresponding to the stored characteristics data shouldbe avoided as a target for the MS^(n) (n≧2) analysis, whether or not theion species should be preferentially selected as a target for the MS^(n)(n≧2) analysis, or whether or not the ion species should be removed uponor prior to the injection of the ion into the mass spectroscopy system),the internal database may be divided or layered in structure in advance.

FIG. 43 shows a diagram of the structure of the mass spectroscopy systemaccording to an embodiment of the invention. The mass spectrometer is aquadrupole ion trap time-of-flight mass spectrometer. A sample solutionseparated in a liquid separating unit 37, such as a liquidchromatograph, is introduced into an ion source (ionization unit) 12where it is converted into a gaseous ion by a spray ionization method,such as the electrospray ionization method and the sonic sprayionization method. The resultant gaseous ion is introduced into adifferential pumping unit 32 via a pore 31. The gaseous ion is furtherintroduced into a high vacuum unit 34 via a pore 33 in which the gaseousion is passed through an ion transportation unit 35 consisting of amultipole pole, for example, and then introduced into an ion trap 20. Aradio-frequency voltage is supplied to the ion trap 20 from aradio-frequency power supply 36 so that the gaseous ion is trapped atthe center of the ion trap 20 by a quadrupole electric field. Withregard to those ions that are not desired to be trapped in the ion trap20 (non-analysis target ions), a radio-frequency voltage can be appliedto the multipole pole in the ion transportation unit in order to removethe ions in the ion transportation unit 35. Further, in cases where themultipole pole is not employed in the ion transportation unit 35, aradio-frequency voltage is applied to the ion trap 20 such that thenon-analysis target ions in the ion trap can be removed by resonancedischarge, for example, and the other ions can be trapped. The gaseousion that has been trapped for a certain period of time is transportedtoward right by an electric force, and then introduced into an ionacceleration unit 38 in a time-of-flight mass spectrometer 21. In theion acceleration unit 38, a pulsed high voltage is applied to theintroduced gaseous ion at a certain timing in order to accelerate thegaseous ion until it has a certain kinetic energy. The acceleratedgaseous ion has its trajectory altered by a reflector 39 and has itsenergy focused, before it is detected by a detector 40. The length ofthe ion trajectory between the ion acceleration unit 38 and the detector40 is predetermined, and the ion velocity is smaller-with increasing m/z(mass/charge number) of the ion. Consequently, the ions are detected bythe detector 40 in the order of increasing m/z. The output of thedetector 40 is fed to an information processing unit where the m/z ofthe ions is determined based on the ion detection time, therebyobtaining a primary mass spectroscopy (MS¹) result. Based on the thusobtained primary mass spectroscopy (MS¹) result, the order of priorityof the ions as the target of the secondary mass spectroscopy (MS²) isdetermined in the information processing unit (data processing unit 15).Thereafter, in order to apply to the ion trap 20 a radio-frequencyvoltage for isolating only those ions that are to become the target ofthe secondary mass spectroscopy (MS²) from the ions introduced into theion trap 20, an instruction is given from the information processingunit (data processing unit 15) to the radio-frequency power supply 36.Further, an instruction for dissociating the isolated ions by CID or thelike is given from the information processing unit (data processing unit15) to the radio-frequency power supply 36, whereby dissociated fragmentions are produced in the ion trap 20. The fragment ions are transportedtoward right by an electric force and then introduced into the ionacceleration unit 38 in the flight-of-time mass spectrometer 21. In theion acceleration unit 38, a pulsed high voltage is applied to the thusintroduced gaseous ion at a certain timing in order to accelerate thegaseous ion until it has a certain kinetic energy. The thus acceleratedgaseous ion has its trajectory altered by the reflector 39 before beingdetected by the detector 40. The output of the detector 40 is fed to theinformation processing unit (data processing unit 15) where the m/z ofthe ion is determined based on the ion detection time. In this way, thesecondary mass spectroscopy is realized. A certain number of theprioritized secondary mass spectroscopy target ions are subjected to thesecondary mass spectroscopy in accordance with the priority order.

Alternatively, the ion trap 20 may employ a linear trap 22 consisting ofa quadrupole, as shown in FIG. 44, instead of the quadrupole ion trap.As compared with the quadrupole ion trap, the linear trap has equivalentfunctionality and is capable of trapping a greater amount of ions atonce. To the linear trap, a radio-frequency voltage is applied such thatnon-analysis target ions can be removed and analysis target ions can betrapped.

Further alternatively, it is also possible to construct the massspectrometer with only a quadrupole ion trap mass spectrometer, as shownin FIG. 45. A sample solution separated in the liquid separating unit 37employing a liquid chromatograph, for example, is introduced into theion source 12 where it is converted into a gaseous ion. The thusproduced gaseous ion is introduced into the differential pump unit 32via the pore 31. The gaseous ion is further passed through, via the pore33, the ion transportation unit 35 installed in the high-vacuum unit 34,and is then introduced into the ion trap 20. A radio-frequency voltageis supplied from the radio-frequency power supply to the ion trap 20 sothat the gaseous ion can be trapped at the center of the ion trap 20. Tothe ion trap 20, a radio-frequency voltage is applied such that thenon-analysis target ions can be removed while trapping the target ions.The gaseous ion that has been trapped for a certain period of time isthen discharged from the ion trap 20 depending on the m/z of the ions,as the radio-frequency voltage applied to the ion trap 20 iscontinuously varied. The discharged ions are detected by the detector40. The output of which is then fed to the information processing unitwhere the m/z of the ions can be determined based on the ion detectiontime (primary mass spectroscopy). The secondary mass spectroscopy mayalso be performed. As compared with the flight-of-time massspectrometer, although the quadrupole ion trap is inferior in terms ofthe range of mass spectroscopy, the mass resolving power, and massaccuracy, it can reduce the size of the apparatus and allows foranalysis with higher sensitivity.

In the embodiments shown in FIGS. 43, 44, and 45, a radio-frequencyvoltage is applied from the radio-frequency power supply in response toan instruction from the information processing unit, whereby thenon-analysis target ions are removed prior to the primary massspectroscopy and the minor components of interest can be reliablysubjected to mass spectroscopy. When the linear trap shown in FIG. 44 isused, in particular, since the volume that can be trapped by the lineartrap is greater than that by the quadrupole ion trap, for example, byapproximately a factor of 8 to two orders of magnitude, the linear trapcan more reliably subject the minor components to mass spectroscopy.

The retention time τ of LC might fluctuate from one measurement toanother. Therefore, one or more kinds of reference substance that isalready stored in the internal database may be put in the sample, andthen the retention time of that reference substance may be compared withan actually measured retention time of the reference substance in orderto obtain a difference Δτ. Then, the retention time of other ion speciesmay be automatically corrected or calibrated for each measurement usingthe difference Δτ. In this way, even when the retention time τ of LCfluctuates from one measurement to another, the target ion species forthe next tandem analysis MS^(n) (n≧2) can be stably selected byutilizing the retention time stored in the internal database.

There are cases where, in the mass-to-charge ratio m/z value, the massaxis (the value of mass-to-charge ratio; m/z) fluctuates as time elapsesfrom the start of measurement. In order to avoid this, one or more kindsof reference substance of which the m/z value is known may be put in thesample and, when there is more than one reference substance, referencesubstances with different retention times of LC and GC may be selected.Then, the actually measured value of m/z of the reference substances andthe known m/z value can be compared so that the m/z value thatfluctuates as time elapses after the start of measurement can beautomatically corrected or calibrated. In this case, as the m/z value isautomatically corrected, it becomes possible to stop the listing ofpseudo-positive reaction sequences when, for example, identifyingpeptides or proteins from the result of measurement of MS data. Thisfunction, however, may be performed in a post-processing step after allthe measurements have been made.

When the ion species that has only been subjected to the tandem massspectroscopy with n=1, namely MS¹, is to be turned into a target for theMS² analysis in the subsequent measurements, the ion species is notregistered in the internal database 10. Namely, the ion species that areto be stored in the internal database 10 are those ion species that havebeen subjected to the tandem analysis MS^(n) (n≧2). In this case, if thesubstance names or structures are known, these information are alsostored in the internal database 10. Upon determination that, with regardto a peptide, a modification structure is attached, informationconcerning the type of the structure and the location where it is added(the amino acid to which the modification structure was attached in anamino acid sequence) may also be stored in the internal database 10.With regard to a peptide derived from a protein that has once beenmeasured and identified, characteristics data, such as the amino acidsequence of the peptide, the name of the original protein, mass numberm, valence z, the mass-to-charge ratio m/z, retention time τ of LC, ionintensity, analysis conditions, and so on, are stored in the internaldatabase 10. These data are automatically stored in the internaldatabase either during or after measurement. Desirably, the storing ofthese data in the internal database 10 should be performed as neededwithin the real time of measurement. However, the storing process doesnot have to be performed within the real time of measurement when theamount to be processed is large, such as when the derivation of peptidesoriginating from proteins is involved.

In the above-described embodiments, the characteristics data of the ionspecies that should not be subjected to tandem mass spectroscopy isstored in the internal database 10 while removing those ion species thatcorresponded to the stored data in the internal database 10 from thetargets of tandem mass spectroscopy. Alternatively, however, thecharacteristics data of the ion species that are desired to be subjectedto tandem mass spectroscopy may be stored in the internal database 10,and the ion species that corresponded to the stored data in the internaldatabase 10 may be selected as the target of tandem mass spectroscopy.

In order to refer to the mass number m of the ion species, instead ofthe mass-to-charge ratio m/z value thereof, as the characteristics dataof the ion species designated prior to or during measurement, in acharacterizing feature of the invention, it is necessary to analyze themeasurement data obtained in the preparation time between theacquisition of the MS spectrum data and the next analysis, or during thetransition time (such as within100 msec, 10 msec, 5 msec, or 1 msec). Asthe mass spectroscopy data (MS^(n))1 represents the ion intensity withrespect to the value of the mass-to-charge ratio m/z, the obtainedmeasurement data is the mass-to-charge ratio m/z. Referring to FIG. 1,in order to derive the mass number m of an ion species from themass-to-charge ratio m/z in the present embodiment, a peak determination2 is carried out on a mass spectrum. Then, on a number Np of peaks thathave been identified as such, an isotope peak determination 3 isconducted. FIG. 6 shows the content of processing in the isotope peakdetermination 3. First, on the peak spectrum data (x=m/z, y=intensity),processes including an enumeration 3-1 of isotope estimation peaks, acalculation 3-2 of the valence and mass number of each ion peak, acalculation of isotope peak intensity distribution and determination 3-3of final isotope peaks are carried out. The content of the enumeration3-1 of the isotope estimation peaks is such that it is determined that,when the interval Δ(m/z)_(i)=x_(i+1)−x_(i) between a peak i(x_(i),y_(i)) and a peak i+1(x_(i+1)(>x_(i)), y_(i+1)) is such thatΔ(m/z)_(i)<1.1, it is estimated that the peak could possibly an isotopepeak that contains one more isotopes than peak i, and if Δ(m/z)i ≧1.1,it is estimated that the peak i+1 is a peak that does not contain anisotope with respect to the peak i. An example of the enumeration 3-1 ofisotope estimation peaks is shown in FIG. 7. With respect to the peakP₁₋₀, three peaks P₁₋₁, P₁₋₂, and P₁₋₃ which are spaced apart from oneanother by Δm/z=1.0 are estimated to be isotope peaks. Similarly, it isestimated that P₂₋₁ is an isotope peak with respect to the peak P₂₋₀ andP₃₋₁, P₃₋₂, and P₃₋₃ are isotope peaks with respect to the peak P₃₋₀.Next, the calculation 3-2 of the valence and mass number of each ionpeak will be described with reference to FIG. 8. In cases where thesample is a peptide or protein, the constituent elements are limited toC, O, N, H, and S. When the natural abundance of these elements and thenumber of these elements included within a peptide are considered, thenumber of isotopes of carbon C is large. The difference in mass numberbetween C¹² and its isotope C¹³ is 1.003354, or approximately 1.0 Da.Thus, in the case where peak i+1 is estimated to be an isotope peak ofpeak i, the valence z of the ion species can be determined from themeasured interval (Δ(m/z)_(i)≈1.0 Da/z) between peak i(x_(i), y_(i)) andpeak i+1(x_(i+1)(>x_(i)), y_(i+1)) (Equation (1)). In this case, since1/Δ(m/z) is not necessarily an integer, a rounding process is carriedout to ensure it is an integer. When the mass number of the ion in aneutral state is m_(p), the mass number is the mass number m_(p) in aneutral state to which the mass number of a proton ion (valence×massnumber mH) is added (Equation (2)).z=1/Δ(m/z)  (1)m/z=(m _(p) +z×mH)/z  (2)

Thus, from Equations (1) and (2), the valence and mass number m_(p) in aneutral state of each ion peak can be determined. In the example shownin FIG. 7, the valence z of ion peak P₁₋₀ is 1 and mass number m=499where m/z=500 Da, as shown in FIG. 8, the valence z of ion peak P₂₋₀ is1 mass number m=512 Da where and m/z=513, and the valence z of ion peakP₃₋₀ is 2 and mass number m=1038 Da where m/z=520. The mass number andvalence of each ion peak may be determined by the above-describedisotope peak determination method. Provided that the intensity of theion peak is sufficiently high (such as when the intensity≧1000), moredetailed determination may be performed based on the intensitydistribution of the peaks without isotopes and the isotope peaks, aswill be described below.

The content of processing in the calculation of isotope peak intensitydistribution and determination of the final isotope peak 3-3 will bedescribed with reference to FIGS. 9A and 9B. For example, when thesample is an amino acid sequence such as a protein or a peptide, theconstituent elements of an amino acid is limited to C, O, N, H, and S.FIG. 9A shows the probability of appearance of each of the 20 aminoacids derived from a protein database (Swiss Prot), and the mass numberof each amino acid. The mass number of amino acid, however, refers tothe mass number of the amino acid (—NH—CR⁰—CO—) in a peptide sequence,where R⁰ is a remaining sequence which differs depending on the type ofamino acid. From these items of data, the average mass number (111.1807Da) of the amino acid and the average values nC, nO, nN, nH, and nS ofeach of the constituent element numbers of the amino acid aredetermined, as shown in Table A in FIG. 9B. Specifically, assuming thatthe protein or peptide is made up of an average amino acid with the massnumber 111.1807 Da as shown in Table A, approximate numbers Nc, No, Nn,Nh, and Ns of the constituent element numbers of C, O, N, H, and S aredetermined from the mass number m of the protein or peptide. Then, theintensity distribution of the isotope peaks is derived. Table B showsthe abundance ratio of each isotope element. Of these isotope elements,the element with the largest abundance ratio is C¹³. Thus, when only theisotope C¹³ is to be considered, the isotope peak intensity for the casewhere the number of included isotopes Nis can be calculated from thefollowing equation:P _(Nis)=[_(Nc)C_(Nis) .pC(1)^((Nc-Nis)) .pC(2)^(Nis) ]×pH(1)^(Nh).pN(1)^(Nn) .pO(1)^(No) .pS(1)^(Ns)  (3)where pC(1), pC(2), pH(1), pN(1), pO(1), and pS(1) indicate theabundance ratios in Table B. FIG. 15 shows an example of the calculationof the intensity distribution of the isotope peaks in accordance withthe mass number using Equation (3). The intensity distribution of theisotope peaks determined from the mass number m calculated in step 3-2is then compared with the intensity distribution of the isotope peaksestimated in step 3-1. If the intensity ratio of the estimated isotopepeaks to the isotope-less peaks corresponds with a less than 50% error,the estimated isotope peaks are finally determined to be isotope peaks.If, on the other hand, the intensity ratio of the estimated isotopepeaks to the isotope-less peaks differs by 50% or more, the estimatedisotope peaks are not determined to be the isotope peaks. In the exampleshown in FIG. 7, the intensity distribution of the isotope peaks isconsidered. Of the estimated isotope peaks, P₂₋₀ where m/z=513 and theestimated isotope peak P₂₋₁, which is displaced by Δ(m/z)=1.0 and with ahigher intensity than that of P₂₋₀, are finally determined to be notisotope peaks, as shown in FIG. 9B. The data obtained in this isotopepeak determination process 3, namely the valence z of each ion peak, themass number m in a neutral state, whether the peak is an isotope peak ornot, and the number of included isotopes Nis, can be outputted in theform of a file or displayed on the display unit 16 along with thedisplay of the spectrum, as shown in FIG. 10. The aforementionedinformation is very useful to the user when determining the target forthe tandem mass spectroscopy or analyzing the spectrum data at the endof measurement.

In the present embodiment, MS^(n+1) is adopted as the next tandem massspectroscopy wherein a parent ion is selected from the MS^(n) ion peaksand is then subjected to dissociation and mass spectroscopy. Adetermination 5 is made as to the presence or absence of any parent iontarget candidate. If there is a parent ion target candidate, the parention for the next MS^(n+1) is determined in a MS^(n+1) analysis contentdetermination 7. In order to allow the parent ion to be selected anddissociated with high efficiency, operating conditions or the like maybe altered and optimized. If there is no parent ion target candidate, anext sample analysis (MS¹) is performed or the measurement comes to anend. At this point in time, the next analysis content (a target ion orthe like, in the case of the tandem mass spectroscopy MS^(n) where n≧2)that has been automatically determined by the invention is displayed bythe display unit 16. If necessary, an interface may be provided thatallows the user to acknowledge the next analysis content beingdisplayed, such that the analysis of the next analysis content that hasactually been automatically determined can be conducted after receivingthe user's acknowledgement.

Furthermore, the invention is characterized in that the above-describedprocesses are carried out at high speed within the real time ofmeasurement. An example of the real time of measurement will bedescribed with reference to FIG. 11, which shows the operation sequenceof the apparatus adapted for tandem mass spectroscopy (MS¹, MS², MS³).According to the invention, analysis conditions such as the voltageapplied to the mass spectroscopy system, the time of introduction ofion, the duration of time of storage of ion, and so on, areautomatically changed or adjusted, depending on the target ion speciesfor MS² or MS³ that has been automatically determined. Whentransitioning from MS¹ to MS², and from MS² to MS³, a series ofprocesses shown in FIG. 1 are carried out within the preparation time ortransition time ΔTp (such as 100 msec, 10 msec, 5 msec, or 1 msec)between the acquisition of the MS spectrum data and the next analysis.For such high-speed processes, a cache memory or hard disc may beallocated for the storage of necessary data. Moreover, the informationprocessing unit may comprise a plurality of information processingunits, such as parallel computers or cluster computers, if necessary. Inthis case, the single internal database 10 may be divided so that thesearch process can be performed in each portion of the internal databasein a parallel manner. Alternatively, in the case where a plurality ofdatabases are provided as the search databases separately from theinternal database 10, the search process may be performed in parallel ineach database. The stored data in the internal database 10 is basicallystored in a hard disc, and when the internal database 10 is used, thecontent of the internal database on the hard disc is written into amemory. In this case, the content of the internal database on the harddisc may be written into the memory regularly at certain time intervals.Prior to measurement, the content of the internal database is writtenfrom the hard disc to the memory, and any content of the internaldatabase that has been added or modified during measurement is added ormodified and then stored in the memory. The content of the internaldatabase may be stored in the hard disc after the end of measurement.While accessing the hard disc may take some time, by transferring thecontent of the internal database to the memory and then accessing thememory, the search of the internal database can be performed duringmeasurement.

When subjecting the sample to mass spectroscopy using LC-MS on thesystem of the invention, a mass spectroscopy measurement process inwhich the sample as the target of analysis is divided into a number nportions (n≧2), and mass spectroscopy is conducted during the time of LCbetween the start of elution and the complete elution of the dividedsample portions, may be repeated n times, n being the number of portionsinto which the sample was divided. In this case, when n=1,high-intensity ion species are sequentially subjected to the MSnanalysis (n≧2), and their characteristics data are stored in theinternal database. Thus, the high-intensity ion species are alreadystored in the internal database when n=2 and thereafter, the other ionspecies, such as low-intensity ion species, that have not been subjectedto the tandem analysis (MS^(n) analysis ((n≧2)) can become the target ofthe MS^(n) analysis (n≧2). Accordingly, an increase can be expected inthe number of proteins identified from the final result of themeasurement process that is repeated n times.

Thus, in accordance with the present embodiment, the spectrum of MS^(n)is analyzed at high speed within the real time of measurement, and it isthen determined whether or not the ion species is the target of the nexttandem mass spectroscopy MS^(n+1) in real time and with high accuracy,so that even minute amounts of ion peaks, as shown in FIG. 3B, can besubjected to tandem mass spectroscopy.

Now with reference to FIG. 12, a second embodiment of the invention isdescribed. In this embodiment, the analysis is limited to minute amountsof peptide and, instead of the collation process 4 with the internaldatabase that is performed in the first embodiment, the intensity ratioof each of the ion peaks in the MS^(n) spectrum to the peak with themaximum intensity is calculated. The peaks with the intensity ratios ofless than 70%, for example, are listed, and the targets for the nexttandem mass spectroscopy MS^(n+1) are determined in real time. It isdesirable, however, to carry out the isotope peak determination in thisembodiment too, in order to eliminate, among the relevant peaks, theisotope peaks from the targets for the next tandem mass spectroscopyMS^(n+1). The intensity ratio with the peak with the maximum intensitymay be entered by the user. In this case, there is no need to carry outthe collation process 4 with the internal database, so that minuteamounts of ion peaks can be determined within the real time ofmeasurement without fail, thereby making it possible to subject minuteamounts of ion peaks to tandem mass spectroscopy.

With reference to FIGS. 3C and 13, a third embodiment of the inventionis described. In this embodiment, MS^(n) is performed again as the nexttandem mass spectroscopy, instead of MS^(n+1). Specifically, an ion peakwith a different m/z value from that of the parent ion that has been thetarget during the measurement of the MS^(n) spectrum is selected fromthe MS^(n−1) ion peaks, and then MS^(n) is repeated. This concept isshown in FIG. 3C. For example, in a case where an ion peak with m/z=1000(m=1000, z=1) is selected as the parent ion in MS¹ and, when an MS²analysis is performed, there is not much dissociation spectrum of MS²and it is determined that the result is insufficient for theidentification of an amino acid sequence, an ion peak with the same massnumber of the target and a different valence (m/z=500, (m=1000, z=2)) isselected in MS¹ as the parent ion, and MS² is carried out again. In thiscase, since the m/z of the parent ion becomes one half, the operationconditions or the like may be changed so as to allow the selection anddissociation of the parent ion to be performed with high efficiency. Bythus repeating MS² on an ion peak with the same mass number of thetarget and a different valence, more often than not a sufficient numberof dissociation peaks for the identification of an amino acid sequencecan be obtained. Further, the present embodiment, as a tandem massspectroscopy function, can be adapted to apparatuses that are equippedonly with the MS² function.

Hereafter, a fourth embodiment of the invention will be described withreference to FIG. 14. In this embodiment, the collation process 4referring to the internal database is not performed, and mainly thedetermination of the isotope peaks is performed. With regard to thepeaks that are determined to be not isotope peaks, the targets for thenext tandem mass spectroscopy may be determined in the order ofdecreasing intensity, as is conventionally done. As shown in FIG. 15,the intensity of isotope peaks becomes greater with increasing massnumber. If the peaks are subjected to tandem mass spectroscopy simply inthe order of decreasing intensity of the peaks, as is conventionallydone, an isotope peak might be erroneously selected as a parent peak. Ifthat happens, the m/z of the mass spectrum is displaced due to theisotope, thereby increasing the likelihood that the result of dataanalysis exhibits a pseudo-positive reaction. In accordance with thepresent embodiment, only those peaks without isotopes are selected asthe targets of the next tandem mass spectroscopy in the order ofdecreasing intensity. Thus, the aforementioned problem is avoided.

Hereafter, a fifth embodiment of the invention will be described withreference to FIGS. 15 and 16. In this embodiment, instead of performingthe isotope determination process 3 as shown in FIG. 6, isotopeintensity distribution patterns corresponding to mass numbers, as shownin FIG. 15, are stored in advance, and the determination as to whetheror not a particular peak is an isotope is made by matching thosepatterns with actual measurement data. The flow of this process is shownin FIG. 16. In accordance with the present embodiment, only the matchingprocess is carried out without performing the isotope peak intensitydistribution calculation in real time, so that it is possible to performthe isotope determination process more reliably in real time.

With reference to FIG. 17, a sixth embodiment of the invention isdescribed. In the embodiments described up to now, when a target ion isselected for the next tandem mass spectroscopy, isotope peaks have beenavoided. However, the selection may be made by including isotope peaks.In this case, the analysis conditions are set such that the resolutionat which a parent ion is selected decreases in accordance with the rangeof appearance of isotope peaks. In the present embodiment, dissociationand mass spectroscopy can be performed on isotope peaks as well, incases where the amount of the parent ion is minute in the first placeand the intensity of isotope peaks is stronger, for example, so that theintensity of the dissociation peak can be increased.

With reference now to FIG. 18, a seventh embodiment of the invention isdescribed. In this embodiment, in cases where the peaks of ion specieswith the same or very close m/z values and with different mass number mand valence z are superposed, the superposition of the multiple ionspecies is determined based on the intensity distribution of isotopepeaks, as shown in FIG. 18. Ion (1) is an ion species with m=1059.7 andz=1. Ion (2) is an ion species with m=2119.5 and z=2. The figure showsan isotope-less peak and isotope peaks for each ion species. When theseion peaks exist simultaneously, they are superposed at the isotope-lesspeak position at m/z=1060.7. If these ion species were subjected totandem mass spectroscopy, the dissociation peaks of the two kinds ofions would appear, thereby making it difficult to perform data analysis,or resulting the result of data analysis estimating an erroneous aminoacid sequence. In accordance with the present embodiment, therefore, onthe assumption that there are cases where the m/z of a plurality of ionspecies is identical, the intensity distributions of their isotope peaksare calculated, and then a distribution is calculated based on thesuperposition of the distributions, as shown in the third chart of FIG.18. The superposed distribution is stored, as shown in the fifthembodiment, and by pattern-matching the stored distribution withmeasured data, it is determined whether or not there is a mixture of aplurality of ion species. When there is a mixture of ion species, theirion peaks are avoided as the targets for the next tandem massspectroscopy in order to prevent the mixture of the dissociation peaksof two kinds of ions which makes it difficult to perform data analysis.In the case where there is a mixture of a plurality of ion species, whenselecting the ion peaks of the multiple ion species as the targets forthe next tandem mass spectroscopy, the possibility is displayed and letknown to the user. Information (m and z) obtained upon determination ofthe mixture of a plurality of ion species may be outputted to a file orthe like so that it can be used for data analysis after the measurementis over.

With reference to FIG. 19, an eight embodiment of the invention will bedescribed. In this embodiment, when, for example, an expression proteinsample from either a healthy subject or a diseased subject is labeledwith an isotope in order to compare the difference in expression levelsby subjecting the peptides from these proteins to an MS¹ analysis, ifthere is an intensity ratio between them, either the isotope-labeledsample or the sample that has not been labeled is selected as the targetfor the next tandem mass spectroscopy. In accordance with the presentembodiment, a peptide derived from a protein with a pathologic potentialcan be automatically determined and subjected to a detailed structuralanalysis.

Now with reference to FIG. 20, a ninth embodiment of the invention willbe described. In this embodiment, instead of performing thedetermination concerning the valence or isotope peaks based on theindividual peak intervals in the measured MS¹ data, as described in thefirst embodiment, and without performing the conversion of the m/z valueof each peak in the measured MS¹ data into mass number m, the massnumber m (such as, for example, m=2000) in the internal database isconverted into a m/z value by simply dividing it by the valence z (suchas, for example, z=1, 2, 3, 4, or 5) within an assumed range. Based onthe thus calculated m/z values (such as, for example, m/z=2000, 1000,666.7, 500, or 400), collation with the internal database is performed.In this case, the processing content becomes much lighter, so that theprocesses can be reliably performed within the real time of measurement.

With reference to FIG. 21, a tenth embodiment of the invention isdescribed. In this embodiment, whether or not each peak in the MS¹ datameasured within the real time of measurement is noise is automaticallydetermined, and those peaks that are determined to be noise are removedfrom a list of valid peaks. For example, in the case where, when thesame sample is subjected to mass spectroscopy a plurality of times atintervals, there is not much difference among most of the peaks in termsof intensity distribution tendencies in each measurement spectrum butthere is a peak that is exhibiting more than 50% intensity fluctuations,as shown in FIG. 21, the greatly fluctuating peak is determined to be anoise peak and automatically removed from the targets for the nexttandem mass spectroscopy. In accordance with the present embodiment, thepossibility of subjecting a noise peak to tandem analysis in caseswhere, for example, the noise peak has accidentally become large can beavoided. Alternatively, in another method for noise determination, if anion species with a certain m/z value is repeatedly detected withintensities exceeding a certain threshold S₀ for more than a certainperiod of time T₀ since the initial detection of the ion species, thation species may be automatically determined to be noise or a peakderiving from impurities. In this case, the certain period T₀ or thecertain threshold S₀ may be designated by the user. Furtheralternatively, a system may be adopted such that, if an ion species witha certain m/z value is repeatedly detected after more than a certainperiod T₀ since the initial detection of the ion species (t=0) (t>T₀),the ion species is removed from the target for tandem analysis (MS^(n)(n≧2)), and if an ion species is repeatedly detected within the certainperiod T0 (t≦T₀), even if that ion species has become a target fortandem mass spectroscopy (MS^(n) (n≧2)) once during this period (t≦T₀)and been stored in the internal database, the ion species can become atarget for tandem mass spectroscopy (MS^(n) (n≧2)) any number of timesas long as t≦T₀. In this case, the results of tandem mass spectroscopy((MS^(n) (n≧2)) obtained from the same ion species are subjected to amerge process in a post-processing.

With reference now to FIGS. 22 a and 22 b, an eleventh embodiment of theinvention is described. As shown in FIG. 22 a, in this embodiment, anion trap mass spectroscopy unit is provided as the mass spectroscopyunit. The structure of the ion trap mass spectroscopy unit is shown inFIG. 22 b. The ion trap is made up of a ring electrode and two end-capelectrodes disposed opposite each other with the ring electrode disposedtherebetween. A radio-frequency (RF) voltage VRFcosΩt is applied acrossthe ring electrode and the two end-cap electrodes. Thus, in the iontrap, there is mainly generated a high-frequency quadrupole electricfield, and the ions vibrate at different frequencies depending on theirm/z values and are trapped (accumulated). When collision induceddissociation (CID) is used as the dissociation method during tandem massspectroscopy, the ion trap itself in which the neutral gas, such as Hegas, is filled functions as a collision cell, there is no need toprovide a separate collision cell. After the target for the tandem massspectroscopy MS^(n) (n≧2) is automatically determined by the presentinvention, the ion species other than the specific ion species with them/z value of the target are caused to be emitted by resonance. Thespecific ion species that are left in the ion trap are caused to vibrateby resonance to such an extent that they are not emitted from the iontrap, thereby causing the ion species to collide with the neutral gasand dissociating the target ion species for the tandem mass spectroscopyMS^(n) (n≧2). During this process, a resonance voltage is appliedbetween the end-cap electrodes. The resonance voltage is a voltage±V_(re) cos ωt with substantially the same frequency ω(≈ω₀) as thevibration frequency ω₀ of the vibration of the specific ion species inthe ion trap and with an inversed phase. Voltages +V_(re) cos ωt and−V_(re) cos ωt are applied to the respective end-cap electrodes.Depending on the mass-to-charge ratio m/z value of the next target ionspecies that has been automatically determined by the system of theinvention, the amplitude value of the high-frequency voltage, thefrequency and amplitude of the resonance voltage, and so on, areautomatically adjusted and optimized during the aforementioned tandemmass spectroscopy. Thus, since the ion trap is capable of carrying outthe tandem mass spectroscopy MS^(n) (n≧2), it can very effectivelyapplied to the system of the invention that automatically determines thenext target.

With reference to FIG. 23, a twelfth embodiment of the invention isdescribed. In this embodiment, an ion-trap, time-of-flight (TOF) massspectroscopy unit is provided as the mass spectroscopy unit. In thiscase, the ion trap is used for the trapping of ions, selection of aparent ion, and as a collision cell, as in the eleventh embodiment.Depending on the mass-to-charge ratio m/z value of the next target ionspecies that has been automatically determined by the system of theinvention, the amplitude value of the high-frequency voltage that isapplied to the ion trap, the frequency and amplitude of the resonancevoltage, and so on, are automatically adjusted and optimized during theabove-described tandem mass spectroscopy, as in the eleventh embodiment.The actual mass spectroscopy is carried out in the TOF portion with highresolution. If it is determined that, based on a collation with theinternal database of the invention, a tandem analysis is necessary, aparent ion is selected and dissociated by the ion trap and is thensubjected to mass spectroscopy in the TOF. If it is determined that notandem analysis is necessary, the parent ion is caused to pass throughthe ion trap and subjected to mass spectroscopy in the TOF. Thus, inaccordance with the present embodiment, the need for tandem analysis canbe automatically determined, so that analysis can be performed with avery high efficiency.

Now referring to FIGS. 24 a and 24 b, a thirteenth embodiment of theinvention is described. As shown in FIG. 24 a, this embodiment ischaracterized in that a linear trap time-of-flight (TOF) massspectroscopy unit is provided as the mass spectroscopy unit. Thestructure of an ion trap mass spectroscopy unit is shown in FIG. 24 b.The linear trap is made up of four pole-shaped electrodes (quadrupoleelectrode) between which a neutral gas is filled. The linear trapfunctions to store ions, select a parent ion, and as a collision cell.Opposed electrodes are considered as a pair of electrodes with the samepotential, and a radio-frequency voltage ±V_(RF) cos ωt of oppositephase is applied across each of the two pairs of electrodes. As aresult, in the linear trap, there is generated mainly a radio-frequencyquadrupole electric field, and the ions vibrate at different vibrationfrequencies depending on their m/z values and are trapped (accumulated).After the target for the tandem mass spectroscopy MS^(n) (n≧2) isautomatically determined by the invention, all of the ion species otherthan the specific ion species with the m/z value of the target areresonance-ejected, and the specific ion species remaining in the lineartrap are caused to resonate and vibrate to such an extent that they arenot emitted from the linear trap, thereby causing the ion species toforcibly collide with the neutral gas and dissociating the target ionspecies for the tandem mass spectroscopy MS^(n) (n≧2). In this case, aresonance voltage is applied across a single opposed pair of electrodes.The resonance voltage is a voltage ±V_(re) cos ωt with substantially thesame frequency ω (≈ω₀) as the vibration frequency ω₀ of the vibration ofthe specific ion species in the ion trap and with an inversed phase.Voltages +V_(re) cos ωt and −V_(re) cos ωt are applied to the respectiveend-cap electrodes. Depending on the mass-to-charge ratio m/z value ofthe next target ion species that has been automatically determined bythe system of the invention, the amplitude value of the high-frequencyvoltage, the frequency and amplitude of the resonance voltage, and soon, are automatically adjusted and optimized during the aforementionedtandem mass spectroscopy. As compared with the twelfth embodiment, theion-trapping rate can be significantly improved (about 8 times). Thus,in accordance with the present embodiment, the content of the nextanalysis is determined based on high-sensitivity data, so thatdetermination can be made with a very high accuracy.

With referent to FIG. 25, a fourteenth embodiment of the invention isdescribed. In this embodiment, a Fourier-transform ion cyclotronresonance mass spectroscopy unit is provided as the mass spectroscopyunit. In the mass spectroscopy unit of the present embodiment, atop-down analysis of proteins can be performed, namely proteins that hasnot yet been subjected to a preprocessing such as enzymatic digestioncan be directly subjected to tandem mass spectroscopy. Thus, the presentembodiment is suitable for the analysis of minute amounts of proteins,for example.

With reference now to FIGS. 26, 27, and 28, a fifteenth embodiment ofthe invention is described. In this embodiment, when the MS^(n) analysis(n≧2) is performed, the information about the ions that have beenanalyzed and the measurement conditions are automatically stored in theinternal database provided inside the mass spectroscopy system, witheach item of data allocated a unique registration number. As shown inFIG. 26, when an n-stage determination 27 is performed where n is 2 ormore, the evaluation 28 of the obtained mass spectrum data is performedand then the information about the ions and the measurement conditionsare automatically stored 29 in the internal database provided inside themass spectroscopy system, with each item of data allocated a uniqueregistration number. As shown in FIG. 27, the registration numberallocated upon storage in the internal database is linked with the massspectrum data that has actually been measured. Thus, at the end ofmeasurement, the user can call the mass spectrum data by clicking theregistration number. In accordance with the present embodiment, the massspectrum data of the ion species of interest can be efficiently referredto by the user, displayed, or outputted in the form of a file. Theinformation about the ion species that is automatically stored includethe registration number, the mass number m of ion, the valence z of ion,and the retention time τ in LC. The measurement conditions include theaccumulation time of the ion species in cases where there is an ionaccumulating portion, such as an ion trap (FIG. 27). As an index for theevaluation of the quality of the mass spectrum data that has beenmeasured, the quality is evaluated in 5 steps in the present embodiment,with the higher quality mass spectrum data being allocated higher indexvalues. Now referring to FIG. 28, an example of the evaluation of massspectrum data is described. Ions that have been temporally separated byLC are detected at the retention times adapted for the individual ions,as shown in FIG. 28A. Although the ions are detected at eachcorresponding time, each ion peak at the detection time has a width ofdozens to hundreds of seconds (FIG. 28B), the mass spectrum data that isobtained differs depending on time even if the ion as the measurementobject has been detected. In the event the MS^(n) analysis is conductedat the initial phase of detection of the ions, or after the ions haveall been detected (i.e., near the foot of the peak in FIG. 28B), theabsolute amount of ions is small, so that it is more likely that themass spectrum data that is obtained is of lower quality with a low S/Nratio (FIG. 28C). On the other hand, if the MS^(n) analysis is conductedat the peak where the amount of ions detected is maximum, it is morelikely that the mass spectrum data that is obtained is of higher qualitywith a high S/N ratio (FIG. 28C). Thus, the quality of the mass spectrumdata of even the same substance differs depending on the time ofmeasurement. In accordance with the present embodiment, therefore, thequality of each mass spectrum data is evaluated and the result isdisplayed, whereby the user can easily determined the quality of eachmeasurement data and perform a highly accurate analysis. In cases wherethe measured object is peptides, the object of evaluation may be theinformation about the amino acids that can be read from the massspectrum data of MS^(n) (n≧2), such as the amino acid sequence or amodified portion. When the information about amino acids is used as theobject of evaluation, the grounds for determination or the data that hasbeen used in determination should preferably be simultaneouslyoutputted. The evaluation of data and the storage of the qualityinformation may be performed after all the measurements have been made.

With reference to FIGS. 29 and 20, a sixteenth embodiment of theinvention is described. In this embodiment, with regard to theinformation about the ion species that has been stored in the internaldatabase, the information about the ion species that can be consideredto be identical is put in order. The ion species with registrationnumbers Nos. 7 to 21 in FIG. 29 can be considered to be the same ionspecies based on the mass number, valence, and the value of theretention time, on the assumption that the tolerance of mass number is±0.05 Da, and the tolerance of retention time is ±1.0 min. In this case,the tolerances may be set by the user. This determination is performedin a internal database storage data processing 30 shown in FIG. 30,whereby redundant data other than specific data is automaticallyeliminated from the database. The specific data includes data withhighest quality, data with higher intensities, or data obtained byadding up a plurality of redundant items of data, for example. Inaccordance with the present embodiment, such redundant data areautomatically eliminated from the database, thereby reducing theredundancy level of the database. With regard to the actually measuredmass spectrum data, too, the data about the ion species that can beconsidered to be identical is eliminated, or a plurality of items of themass spectrum data about the ion species that can be consideredidentical are added into a single item of data in the internal DB storeddata processing 30. With regard to the data processing in the presentinvention, it is also possible to perform the processing after all ofthe measurements have been made. The consolidation of the redundant datain the database may be performed across a plurality of databases bycomparing the stored data in the individual databases.

With reference to FIG. 31, a seventeenth embodiment of the invention isdescribed. In this embodiment, when the MS^(n) (n≧3) is performed, themass spectrum data of MS² and the mass spectrum data of MS^(n) (n≧3) areadded. Alternatively, when, in the case where there was a peak with thesame mass number m as the target ion species during the MS² but with adifferent valence (namely, a different m/z value), the MS² has beenrepeated by using that peak as the target (parent ion) instead of theMS^(n) (n≧3) analysis, the mass spectrum data of the first MS² and themass spectrum data of the second MS², which have been obtained by usingas the targets the peaks with the same mass number and differentvalences, are added. When the object of measurement is a peptide, adatabase search is generally used for the analysis of the resultant massspectrum data. However, the database used for the database search isconstructed on the basis of the MS² analysis data, and it is difficultto use the MS^(n) (n≧3) analysis data as is. Accordingly, in accordancewith the invention, when the MS^(n) analysis is performed, it ispossible to combine the mass spectrum data of the MS² and the massspectrum data of the MS^(n) (n≧3) in the internal DB stored dataprocessing 30 as shown in FIG. 30. In this case, a certain weight may beadded to the MS^(n) data that is combined. In accordance with thepresent embodiment, the user can analyze the MS^(n) measured massspectrum data easily using the database search. The data processing inaccordance with the present invention may be performed after all themeasurements have been made.

With reference now to FIG. 32, an eighteenth embodiment of the inventionis described. In this embodiment, the mass spectrum data obtained byusing different dissociation methods are added. When the mass spectrumdata is measured from the same ion using different dissociation methods,the dissociation efficiency or the obtained tendency of the ion differdepending on the dissociation methods. Thus, by combining data obtainedby different dissociation methods and then analyzing the combined data,it can be expected that the measurement object can be identified withhigher accuracy. A case will be described in the following where massspectrum data is obtained using collision induced dissociation (CID) andelectron capture dissociation (ECD). When the object of measurement is apeptide, use of CID as the dissociation method result in the detectionof mainly b and y ions. On the other hand, it has been reported that useof ECD resulted in the detection of mainly c and z ions. Thus, inaccordance with the invention, a plurality of data obtained by usingdifferent dissociation methods are added in the internal DB stored dataprocessing 30 shown in FIG. 30. In accordance with the embodiment, theidentification accuracy can be expected to improve, and it can also beexpected that the probability of identification of ions, which has beendifficult by the aforementioned methods individually, is improved. Thedata processing in the present embodiment may be performed after all ofthe measurements have been made.

With reference to FIG. 33, a nineteenth embodiment of the invention isdescribed. In this embodiment, when performing the addition of aplurality of mass spectrum data in the internal DB stored dataprocessing 30 shown in FIG. 30 (such as that in embodiments 17 and 18),the user is allowed to designate the ratio of addition. For example,when there is only a minute amount of ions that are to be analyzed, byvarying the ratio of addition, the analysis of mass spectrum data can beperformed by taking into consideration the amount of the parent ion tobe dissociated. Although in the present embodiment the processinginvolves two pieces of data, more than two pieces of data may besimilarly designated. In accordance with the embodiment, more accurateanalysis can be performed in which the fragment intensity is taken intoconsideration. The data processing in the present embodiment may beperformed after all the measurements have been made. The presentembodiment may be adapted such that the entire MS measurement data isconverted into monovalent ion data.

With reference now to FIG. 34, a twentieth embodiment of the inventionis described. In this embodiment, the intensity of the ions that havebeen determined to be isotope peaks can be added to a monoisotopic peak.As described with reference to the first embodiment of the invention,the intensity of the isotope peaks determined from the ion intensity andpeak interval is added to the intensity of the monoisotopic peak in theinternal DB stored data processing 30 shown in FIG. 30. In accordancewith the present embodiment, more accurate analysis can be performed inwhich the entire intensity of the ions as the object of measurement istaken into consideration. The data processing in the embodiment may beperformed after all the measurements have been made.

In the following, a method of correcting the mass in analysis data isdescribed as a 21^(st) embodiment of the invention. In the shotgunanalysis of proteins, for example, external databases of genes orproteins are searched based on the result of mass spectroscopy in orderto finally identify the chemical structure, for example, of biopolymers.In this case, the higher the accuracy of the mass of the ion that hasbeen analyzed, the more accurately and efficiently the identification ofbiopolymers can be made. Thus, for such analysis, it is important to usea time-of-flight (TOF) mass spectrometer or Fourier transform ioncyclotron resonance (FTICR) mass spectrometer, which have a relativelyhigh mass accuracy. However, the mass accuracy of the time-of-flight(TOF) mass spectrometer can be affected by the room temperature of thelocation where the equipment is installed. Should the mass accuracyfluctuate more than expected for one reason or another, the biopolymermight not be accurately identified even if the external-database searchis conducted. For this reason, an internal reference substance of whichthe m/z of a detected ion is known is often analyzed in advanceimmediately prior to analysis, and the m/z of the mass spectrometer iscalibrated based on the result of the prior analysis. However, there isthe possibility that, in LC/MS where analysis is conducted continuouslyfor hours on end, the mass accuracy might fluctuate more than expected.Thus, if a known ion of which the mass-to-charge ratio m/z is known inadvance is detected in the ions detected by mass spectroscopy, the m/zof the other detected ions can be corrected based on the informationabout the known ion. By detecting a plurality of known ions, theaccuracy of the m/z after correction can be improved greatly. Oneproblem of this method is that it is bothersome, as the analysis datamust be corrected by a kind of manual operation. If, however, there isinformation available in the internal database 10 concerning the m orm/z of the ions that could be detected or the retention time τ of LC,the known ions detected by MS¹ could be identified using thatinformation. By identifying a plurality of known ions, the temporalfluctuation of m/z could also be predicted by information processingtechniques, so that the m/z of the analyzed ions could be automaticallycorrected. This means that data of high mass accuracy can be easilyacquired even if the mass accuracy of the mass spectrometer fluctuatesmore than expected. Moreover, when a mass spectrometer equipped withthis type of information processing function is employed, the need foranalyzing known substances prior to analysis can be eliminated, so thatthe burden on the user can be reduced. Thus, the information stored inthe internal database 10 can be substantially and effectively utilizedfor the calibration or correction of the m/z of analysis data, as wellas for the control of the real-time mass spectrometer.

(Real-time Fast De Novo)

Hereafter, a 22^(nd) embodiment of the invention is described. FIG. 35 ashows a flow chart of a comparative example involving the use of tandemmass spectrometer, starting with the analysis of a protein and endingwith the identification of the protein. A protein sample is renderedinto a peptide sample fragmented by enzyme digestion, for example. Thepeptide sample is then separated LC or GC and then ionized. Thereafter,a mass spectroscopy (MS¹) is carried out, and a precursor ion (parention) to be subjected to a MS² analysis is selected from the detectedions. After the selected precursor ion is dissociated, a massspectroscopy (MS²) is carried out, thereby obtaining mass spectrum data.The resultant mass spectrum data is subjected to a data processing (48)in a post-processing after the end of measurement, where noise peaks andisotope peaks are removed and the valence of ions is determined, forexample. Then, a database search (49) is conducted using a proteindatabase consisting of known proteins. In this identification flow,since the analysis of the obtained MS² mass spectrum data is performedin a post-processing after the end of measurement, the validity of theMS² mass spectrum data cannot be determined on a real-time basis duringmeasurement. Meanwhile, it is important to obtain as much information aspossible in a single measurement in cases where there is only anextremely minute amount of sample available, such as a diseased protein,for in such cases it is difficult to repeat mass spectroscopy.

Thus, in accordance with the present invention, the MS^(n) (n≧2) data isanalyzed on a real-time basis (i.e., during the operation of the massspectroscopy apparatus), and then the content of next analysis isdetermined based on such analysis, so that the analysis flow can beoptimized. By “on a real-time basis” herein is meant the analysis isperformed within a preparation time or transition time ΔTp between thetime when the MS spectrum data is obtained and the time when the nextanalysis starts (such as, for example, 100 msec, 10 msec, 5 msec, or 1msec). FIG. 35 b shows a flowchart of the present embodiment wheretandem mass spectroscopy is employed, starting with the analysis of aprotein and ending with its identification. This flow differs from theconventional flow shown in FIG. 35 a in that the acquired MS² massspectrum data is analyzed during measurement, and the result of analysisis fed back for the determination of the content of the next analysis.The data analysis of the acquired MS² mass spectrum data duringmeasurement and the determination of the next analysis content based onthe result of analysis are implemented in the control unit 17 or dataprocessing unit 15 in the mass spectroscopy system shown in FIG. 2. FIG.36 shows a detailed flowchart of the processes performed in the dataprocessing unit 15 during the data analysis of the acquired MS² massspectrum data during measurement and the determination, which isautomatically performed, of the next analysis content based on theresult of analysis. As shown in FIGS. 2, 35 b, and 36, after the proteinsample that has been fragmented by enzyme digestion or the like isseparated by LC or GC, the sample is ionized and then subjected to massspectroscopy (MS¹) in the mass spectroscopy unit 13. Based on the resultof the mass spectroscopy (MS¹), a specific ion (parent ion) is selected,and the parent ion is dissolved in a collision cell 13A (Selection anddissociation 45 of parent ion). The resultant dissociated fragment issubjected to mass spectroscopy (MS^(n): n≧2) in the mass spectroscopyunit 13. Then, for the resultant MS^(n) (n≧2) mass spectrum data, a peakdetermination 2 and an isotope peak determination 3 are conducted in thecontrol unit 17 or data processing unit 15, as shown in FIG. 36.Further, a peak interval extraction 53 corresponding to the mass numberof a particular amino acid is carried out, and then a scoring 54 iscarried out in terms of the mode of dissociation (such as, for example,a ion, b ion, c ion, x ion, y ion, and z ion) or based on the degree ofcorrespondence to the mass number derived from a particular amino acidsequence, followed by a decoding 55 of the amino acid sequence. Aminoacids that have been decoded herein refer to those amino acids withscores in the scoring 54 that exceed a certain designated value.Thereafter, the content of the next analysis is determined in accordancewith the number of the decoded amino acids (56). If the number ofdecoded amino acids exceeds a certain designated number, it is assumedthat sufficient information necessary for analysis is contained in theMS^(n) (n≧2) mass spectrum data, and the MS¹ of the next elation sample,or the MS² measurement of another parent ion is terminated. On the otherhand, if the number of the amino acids that could be decoded does notreach the designated number, it is assumed that the informationnecessary for analysis is not sufficiently contained in the MS^(n) (n≧2)mass spectrum data and a selection 57 a, 57 b of a specific dissociationion (precursor ion) is automatically performed, and the ion is subjectedto the MS^(n+1) (n≧2) analysis or MS^(n′) (n≧2) analysis is performed.The MS^(n′) analysis herein refers to the repetition of the MS^(n)analysis in the event that the peak of an ion species with substantiallythe same mass number m and a different valence z from those of theparent ion that has been selected and dissociated during the acquisitionof the MS^(n) data is observed in the MS^(n−1) spectrum data, in whichrepetition that ion species is selected as the parent ion. In theMS^(n+1) (n≧2) analysis or MS^(n′) (n≧2) analysis, different standardsare employed in the automatic selection of the parent ion (57 a, 57 b).In the case of the MS^(n+1) (n≧2) analysis, the parent ion is selectedby giving priority to those of the peaks containing amino acids and withlower scores allocated in the scoring 54 that have a greater m/z or massnumber, or to y ions. In the case of the MS^(n′) (n≧2) analysis, theparent ion should preferably be selected from those ion species withsubstantially the same mass number m and a different valence z fromthose of the parent ion that has been selected and dissociated duringthe acquisition of the MS^(n) data. If possible, the parent ion shouldpreferably be selected from ions with a greater valence than that of theparent ion that has been selected during the MS^(n) analysis. This isbecause of the knowledge that the greater the valence, the moredissociation fragments can be obtained (V. H. Wysocki, G. Tsaprailis, L.L. Smith and L. A. Breci, J. Mass Spectrom. 35, 1399 (2000)).

Preferably, when performing the MS^(n+1) analysis or MS^(n′) analysis,in cases where the valence of the parent ion of the MS^(n) mass spectrumdata to be analyzed is 1 and its mass number is Mp, the MS^(n′) analysisis preferentially performed if an ion peak is being detected in theMS^(n−1) mass spectrum data that has a mass number Mp and a valence of 2or more, by using the ion species of that ion peak as the parent ion. Ifthe valence of the parent ion in the MS^(n) mass spectrum data isalready 2 or more, preferably the MS^(n+1) analysis shouldpreferentially be performed. This is in consideration of the followinghypothesis. Namely, when the valence is 1, if a basic amino acid such asarginine (R) or lysine (K) is included in the sequence, protons arestrongly strapped by such a basic amino acid, and many peptides do nothave protons (mobile protons) that can freely move around within themain chain of the amino acid sequence. These mobile protons are said tohave a large influence on the dissociation of the bond between aminoacids (see the above-cited reference). Peptides that do not have amobile proton are hard to be cut, resulting in the MS² spectrum datatending to have a smaller number of dissociation ion peaks. On the otherhand, in the case of a multivalent ion, to which a plurality of protonsare attached, even if one proton H⁺ is strongly trapped by the basicamino acid, other protons H⁺ are more likely mobile protons that canmove around, so that the probability of the peptide being dissociated ateach bond between the amino acids increases. The selection of theMS^(n+1) analysis or the MS^(n′) analysis may be made by the user viathe user input unit. The result of determination in the control unit 17or the data processing unit 15 is utilized through an overall controlunit 17 as the next analysis information. Depending on the next analysisinformation, operation conditions, such as the voltage applied to themass spectroscopy unit 13, are automatically optimized by the overallcontrol unit 17.

With reference to FIG. 37, an example is described where theidentification accuracy is improved by performing mass spectroscopy inaccordance with the flow of the invention.

In this embodiment, of the processes performed in the data processingunit 15, the MS^(n) (n≧2) mass spectrum analysis process (thedetermination of isotope peaks and valence, the decoding of the aminoacid sequence, and the determination of the next analysis content in thecase where the number of amino acids that has been decodes does notreach a certain value) is performed within 10 msec (or 100 msec). Asample 41 introduced from an introduction unit was separated (42) by LCand then ionized (43) in an ionization unit. As the ionization method,the ESI (electro-spray ionization) process was used. The ionized samplewas then subjected to mass spectroscopy (MS¹) in the mass spectroscopyunit (44). Of the ions that were detected in an ion detection unit,specific ions (with m/z=808) were subjected to the selection anddissociation in the ion trap (45), and mass spectroscopy (MS²) wasperformed (46). On the obtained MS² mass spectrum data (47), the peakdetermination 2, the determination of isotope peaks and valence, theelimination of isotope peaks 3, and the conversion of valence wereperformed, and thereafter the decoding 53 of the amino acid sequence wasconducted. In the present embodiment, the number of amino acids that aredecoded for the determination was set to be 5. If the number of theamino acids that have been decoded is less than 5, the MS³ analysis (58)or the MS^(2′) analysis (59) is performed. During the decoding of theamino acids, it is first determined (53) whether the mass peak intervalcorresponds to the mass number of the amino acid within a certain rangeof tolerance. If it does correspond, it is next determined what type ofdissociation the corresponding peak of the ion has (54). In the presentsystem, a score is given depending on the type (such as a ion, b ion, cion, x ion, y ion, or z ion) of dissociation of the detected ion suchthat the types of ion that are more likely detected are allocated higherscores. For example, when the dissociation method is CID, b ion and yion are given higher scores, and when the dissociation method is ECD, cion and z ion are given higher scores. The tolerance for the mass andthe scoring parameters can be changed by the user depending on variousconditions, such as the type of the apparatus and the method ofdissociation. Moreover, in cases where the likelihood of dissociationoccurring between the amino acid sequences (the ease with which they arecut) is evaluated in advance in an experiment or simulation, thatinformation may be used as a database for the decoding of the amino acidsequence. In that case, since the information about the intensity of themass spectrum data can be incorporated during the determination, thedecoding of the amino acid sequence can be more accurately performed.Thereafter, with regard to the mass peak interval that is within thetolerance and that has been determined to be possessing a score thatexceeds a certain value, the decoding of the amino acid (55) isperformed based on the m value of the parent ion, starting from both theN and C terminals of the peptide, and the number of amino acids thathave actually been decoded is derived.

In the present system, after the elimination of isotope peaks, thedetermination of valence, and the conversion of the valence value areperformed on the resultant MS² mass spectrum data in the data processingunit 15, the amino acid sequence is decoded. In this system, it is thendetermined if the number of the amino acids that have been decodedreaches a specified value (56). If not, the next analysis content isdetermined based on either the MS³ analysis or the MS^(2′) analysis.Whether the MS³ analysis or the MS^(2′) analysis should be performed maybe designated by the user at the beginning. In the present example, thesystem is set such that the MS³ analysis is selected as the nextanalysis. If the routine should proceed to the MS³ analysis (58), a peakwith a low-score region (estimated amino acid) is preferentiallyselected as the parent ion (57 a). When the dissociation method is CID,peaks that can be thought to be y ions are preferentially selected. Thisis due to the fact that, in an enzymatic digestion by tryptin, arginine(R) or lysine (K), which readily trap protons, is located at the Cterminal, making it easier for y ions to be detected with highintensity. On the other hand, in the case of the MS^(2′) analysis (59),although the MS² analysis is performed once again on the ion with thesame mass number m and a different valence z, if there is an ion with alarger valence z, that ion is preferentially selected as a precursor ion(57 b). If bivalent ions are selected as precursor ions, most of theresultant dissociation fragments would be detected as monovalent, sothat the data analysis in a post-processing step would be easier. If thevalence of the ion analyzed in the MS² analysis is monovalent, bivalentions are preferentially selected as precursor ions for the MS^(2′)analysis. When the MS^(n+1) (n≧3) is repeated, depending on the analysisresult, the mass number of the precursor ion gradually decreases.Therefore, the user may be allowed to choose, via the user input unit,to change the number of the decoded amino acids to be determineddepending on the mass number of the parent ion, or to proceed to thenext measurement or end the measurement if the mass number of the parention drops below a predetermined value.

In the present embodiment, an ion with m/z=563.2 was selected as theparent ion for the MS³ analysis. The thus selected ion was dissociatedand then subjected to the MS³ analysis. When the amino acid sequencedecoding process was performed again on the resultant MS³ mass spectrumdata, seven amino acids were decoded. In the present embodiment, it tooknot more than 10 msec for any of the mass spectrum analysis processes,suggesting that the mass spectrum can be evaluated and determined on areal-time basis during the measurement of the mass spectrum data. Asshown in FIG. 37, the MS² mass spectrum data per se, and mass spectrumdata obtained by mixing the MS² mass spectrum data and the MS³ massspectrum data was subjected to analysis using a database search software(MASCOT) (due to the fact that the current database is only adapted forthe MS² mass spectrum data). In the analysis using the MS² mass spectrumdata, the correct sequence (MIFVGIK) was ranked below the 10^(th) place.In the analysis using the MS²/MS³ mixed mass spectrum data, however, thecorrect sequence was ranked first. These results indicate that theidentification accuracy of a measurement target can be improved by thepresent invention.

In accordance with the invention, for the MS^(n) mass spectrum data inwhich the amino acid sequence can be decoded with more than a certainvalue, the routine proceeds to the measurement of the next sample (MS¹or MS² using another ion as the parent ion) instead of performing theMS^(n+1) or MS^(n′) analysis. Thus, wasteful measurement can be avoidedand analysis can be performed with a high throughput. Further, theinvention can be applied to any compounds with equivalent effects aslong as the compounds have a limited kinds of basic structures asstructural units, such as proteins with sugar chains or modifyingstructures, or polymers.

(Real-time Database Search)

A 23^(rd) embodiment of the invention will be described in thefollowing. For the identification of proteins, methods that utilize a denovo peptide sequence process and methods that utilize a database searchare available, of which a database search method will be describedbelow. In the present embodiment, a database search is conducted on theMS^(n) mass spectrum data obtained on a real-time basis. FIG. 38 shows aflowchart of the processes performed in the present embodiment. On theMS^(n) (n≧2) mass spectrum data that is obtained, a database search isconducted on a real-time basis during measurement, using a largedatabase that stores the mass numbers of the peptide sequences obtainedby enzymatically digesting the sequences of many of the known proteinsthat are registered in public databases, for example, and the massnumbers of all of the dissociation fragment peptides predicted from suchpeptide sequences. By “on a real-time basis” herein is meant that theMS^(n) (n≧2) mass spectrum analysis process (the determination ofisotope peaks and valence, the database search 60, and, in the casewhere n>2, the addition of the MS² mass spectrum data and MS^(n) massspectrum data) is performed within 10 msec (or 100 msec). If in thedatabase used for the database search 60 there is only data availablethat corresponds to the MS² mass spectrum data, the MS^(n) (n>2) massspectrum data must be added to the MS² mass spectrum data. In thedatabase search that is performed in a conventional post-processingstep, the search takes approximately one minute per spectrum. However,real-time analysis can be realized by adopting a parallel computer or aPC cluster in the data processing unit 15 in order to process data in aparallel manner, or by dividing the database so that the database searchcan be performed in a parallel manner and at higher speed.

(Specific Conditions→MS³/MS^(2′))

A 24^(th) embodiment of the invention will be described in thefollowing. FIG. 39 shows a flowchart of the processes performed in asystem according to the present embodiment. In this embodiment, if theMS^(n) data that has been real-time analyzed satisfies conditionsspecified by the user, for example, the MS^(n+1) analysis or the MS^(n′)analysis is performed. Table 1 shows the mass number of individual aminoacid residues, and the mass number of dipeptides in which two aminoacids similar to the individual amino acid residues are bonded.

TABLE 1 Single amino acid Mass number Double amino acid Mass numberresidue (Da) residue (Da) Trp 186.2 Glu-Gly 186.2 Ala-Asp 186.2 Ser-Val186.2 Lys-Gly 185.2 Gln-Gly 185.2 Asn-Ala 185.2 Asn 114.1 Gly-Gly 114.1Lys 128.2 Gly-Ala 128.1 Gln 128.1 Gly-Ala 128.1 Glu 129.1 Gly-Ala 128.1Arg 156.2 Val-Gly 156.2

It will be seen from Table 1 that the mass number of lysine (Lys) andthat of a dipeptide (Gly-Ala or Ala-Gly) consisting of glycine (Gly) andalanine (Ala), for example, are substantially identical and would beindistinguishable in equipment with low resolution. Thus, in thereal-time analysis of the MS² (n≧2) mass spectrum data in Embodiment 22(real-time de novo), if it is determined that there is the possibilitythat the data could include an amino acid, such as Lys, whose massnumber is expected to be equal to the sum of the mass numbers of twoamino acid residues, the MS^(n+1) analysis or the MS^(n′) analysis canbe automatically performed. Table 2 shows examples of the chemicalmodifications of amino acids.

TABLE 2 Type of chemical modification Δm (Da) Formylation 28.01Phosphorylation 79.98 Acetylation 42.04 Myristylation 210.36Hydroxylation 15.99 Glycosylation (when the sugar is 162.14 hexose)

As shown in Table 2, if there is the possibility that a modifyingstructure, such as a phosphoric acid, is attached to the amino acid, theMS^(n+1) analysis or MS^(n′) analysis can be performed by using a peakfrom which the modifying structure is detached as a parent ion. Asequence, such as glycine (Gly)-glycine (Gly), that is considered totend to not produce dissociation (i.e., that is considered to be hard tobe cleaved) is inputted in the sequences in advance, and it is thendetermined if there is the possibility the aforementioned sequence, or asequence designated by the user, is contained (61). It is determinedthat there is the possibility that the particular amino acids orsequence is contained, ions that contain such amino acids or sequenceare selected as a parent ion (62) and then the MS^(n+1) analysis orMS^(n′) analysis can be performed. These conditions may be entered bythe user via the user input unit. By performing the MS^(n+1) analysis orMS^(n′) analysis only when specific conditions specified by the user aresatisfied, tandem mass spectroscopy data can be obtained that containsmore detailed structural information. Moreover, the amino acid sequenceanalysis method according to the present embodiment may be performed ina post-processing step, rather than on a real-time basis. Generally,when analysis is performed on the entire data including those massspectrum data with smaller amounts of information and with lowerreliability in a database search, not only does it take longer for thesearch but also there is the possibility of identifying pseudo-positiveproteins. Thus, it is better in some cases to eliminate mass spectrumdata with lower reliability. By so doing, it would become possible toevaluate, using the amino acid sequence analysis method of the presentembodiment, if particular data in a huge amount of data contains a largeamount of information and whether or not it is highly reliable. In thisway, only mass spectrum data with high reliability could be used for thedatabase search, so that analysis could be performed more reliably andat higher speed than possible by conventional techniques.

(Determination by the Number of Peaks and By Peak Groups)

Hereafter a 25^(th) embodiment of the invention is described withreference to FIGS. 40 to 42. FIGS. 41 and 42 show flowcharts of a systemaccording to the present embodiment. When a peptide is analyzed using adatabase search, even if not all of the dissociation fragments predictedfrom the amino acid sequence of the peptide are obtained, the peptidecan be identified as long as a certain number of peaks of fragment ionsare obtained. Thus, the amount of information possessed by the massspectrum data can be determined based on the number of peaks of thedissociation fragment ions. As shown in FIG. 40, when one or more masspeaks are detected that are inferred to be derived from an amino acid,such as a dehydration peak or deammoniation peak from the peaks inferredfrom the decoded amino acid sequence, these peaks are processed asconsisting of one and the same kind, and then the number of such groupsof peaks of the same kind is derived. Alternatively, a group of peaksthat appear in a range of m/z (such as the range of m/z=±40 with respectto the m/z value of the peak of b ion or y ion, for example) in whichthe possibility of appearance of dehydration peaks or deammoniationpeaks derived from a single amino acid is high may be processedtogether, and then the number of such peak groups may be obtained. It isthen determined in a determination 63 whether or not the number of suchpeak groups exceeds a certain number or no. If it does, the massspectrum data is considered to contain an amount of informationnecessary for identification, and then the measurement (MS¹, or MS²using another ion as a parent ion) of the next sample is performed, orthe measurement comes to an end. The number of the peak groups may beentered via the user input unit. On the other hand, if the number of thepeak groups does not reach the certain number, the MS^(n+1) analysis orthe MS^(n′) analysis is performed. In this case, in a selection 64 ofthe parent ion for the MS^(n+1) analysis, of those peak groups in whichthe interval between the individual peak groups is the largest, a peakwith a strong intensity is selected from the group of peaks with largem/z values. In this way, the MS^(n+1) analysis can be performed on ionscontaining some portions of which peaks are not detected and in whichthe amount of information is small, so that the accuracy ofidentification can be expected to improve. This determination is notperformed on the peak groups; rather, the number of peaks with valuesexceeding a certain threshold is determined (65), and it is thendetermined if the number of such peaks is more than a certain number(66). If the number of the peaks is more than the certain number, it isassumed that the mass spectrum data contains sufficient amount ofinformation necessary for identification, and the measurement of thenext sample (MS¹, or MS² using another ion species as the parent ion),or the measurement comes to an end. On the other hand, if the number ofthe peaks does not reach the certain number, the MS^(n+1) analysis orthe MS^(n′) analysis is performed. In this case, in a selection 67 ofthe parent ion for the MS^(n+1) analysis, simply a peak with thestrongest intensity is selected as the parent ion. In this way, theMS^(n+1) analysis can be performed on the ions containing portions ofwhich the peaks are not detected and with a small amount of information,so that the accuracy of identification can be expected to improve. Thethreshold value and the number of peaks may be designated by the uservia the user input unit.

(Sugar Chain as the Object of Measurement)

A 26^(th) embodiment of the invention will now be described. When thesample is a sugar chain, its structural unit is a monosaccharide. Thus,in the analysis of the MS^(n) mass spectrum data, the relevantmonosaccharide is inferred from the mass peak intervals. In thisembodiment, as in Embodiment 22 (real-time de novo), the MS^(n) massspectrum data on which the elimination of isotope peaks, thedetermination of valence and the conversion of valence have beenperformed is processed to extract the peak intervals within a certaintolerance range or with a score of more than a certain value, and thenthe number of monosaccharides that can be decoded from the terminal ofthe sugar chain is derived. When the number of the monosaccharides thathave been decoded is more than a certain value specified by the user,for example, the measurement of the next sample is conducted, or themeasurement is terminated. On the other hand, if the number of themonosaccharides that have been decoded does not reach the certain value,the MS^(n+1) analysis or the MS^(n′) analysis is performed. As theparent ion for the MS^(n+1) analysis, peaks containing regions withlower scores are preferentially selected. The above-described processesare carried out within the real-time of measurement (such as within 10msec or 100 msec), and an optimum analysis flow is automaticallyselected.

FIG. 46 shows a system based on an embodiment of the mass spectroscopysystem of the invention. An input operation for a first databaseconcerning the analysis object ion is conducted on a terminal devicesuch as a personal computer. If it is necessary to create a file for anew database, while the mass of ion (or m/z, where m is the mass of ionand z is ion charge) may be directly entered on the computer screen, itis also possible to select and enter information (such as the categoryof the species (such as humans), the digestive enzyme, the presence orabsence of modification, organs, etc.) for utilizing external databases.In the latter case, it is also possible to create or update the databaseusing a server to which an external database of genes or proteins hasbeen downloaded, or via the Internet. When existing databases areutilized, a first database is determined by, for example, selecting froma list of existing databases on the screen. After necessary inputinformation about the first database has been entered, a transmit inputis performed. By these operations, the first database in which thecandidate substances as analysis targets are recorded is stored in adatabase storage unit. In an actual analysis, in order to make itdifficult for the ions of substances that are not listed in the firstdatabase to be detected, an instruction for controlling the RF voltageto be applied to the mass spectrometer (MS) may be transmitted from theinformation processing unit to the RF voltage power supply before theprimary mass spectroscopy is performed. In this manner, before any ionof a substance that is an analysis target candidate listed in the firstdatabase is detected in the primary mass spectroscopy, the unwanted ioncan be discharged. The information about the detected ions is searchedfor as needed in the first database that is stored in the databasestorage means. As the number of types of ions that can be the targetsfor the secondary mass spectroscopy is limited, an instruction is sentfrom the information processing unit to the power supply involved withCID such that those ions that correspond to the data in the firstdatabase are preferentially subjected to the secondary mass spectroscopy(tandem mass spectroscopy). If the ions for which no analysis isnecessary are known, a secondary database for recording the data aboutanalysis target candidate substances may be created in the same manneras in the case of the first database, and the secondary database may beused for controlling the RF voltage applied during the primary massspectroscopy. Further, the information about those ions listed in thefirst database for which analysis has been completed can be transferredto the second database. By so doing, redundant analysis of the same ioncan be avoided, thereby allowing minute samples of more kinds of ions tobe analyzed. Identification of a particular substance is performed basedon the result of the secondary mass spectroscopy and the informationabout the parent ion therefor.

FIG. 47 shows an example of the flow of the aforementioned analysis. Inthis example, the number of times that tandem analysis can be performedin a single sequence is N, and the information about those ions listedin the first database that have been detected k times is deleted once byupdating the first database. Such automatic updating of the database maybe designated by an operation on the screen (i.e., an input screen onthe display unit) shown in FIG. 46 prior to the start of analysis. Whenanalyzing an extremely minute amount of a target sample, it would bemore advantageous to turn off the automatic updating of the firstdatabase from the viewpoint of detection of the analysis target sample,as shown in FIG. 48.

FIG. 49 shows the flow of an embodiment in which a second database isprovided. When a non-analysis target ion of which the ion intensity isexpected to be very strong is known, the information about thenon-analysis target ion may be stored in a second database that can becreated in the same manner as in the first database, and the informationmay be usefully used for the control of the RF voltage applied duringthe primary mass spectroscopy. These settings of the flow may be made byoperations on the screen (i.e., input operations on the display unit)shown in FIG. 46.

FIG. 50 shows a diagram of an apparatus according to an embodiment ofthe mass spectroscopy system of the invention. The apparatus comprises aquadrupole ion trap time-of-flight mass spectrometer, which is acombination of a quadrupole ion trap and a time-of-flight massspectrometer and is described in Analytical Chemistry, Vol. 67 (1995)pp. 234A-242A, for example. However, the present embodiment is unique inthat the trajectory of ions discharged from the ion trap is bent atsubstantially right angle at an acceleration portion of thetime-of-flight mass spectrometer. This configuration is adopted so thatthe spread of energy of ions at the acceleration portion of thetime-of-flight mass spectrometer can be reduced and the mass resolutioncan be improved. A sample solution separated in a liquid separationportion of a liquid chromatograph, for example, is introduced into theion source where it is turned into a gaseous ion by a spray ionizationprocess, such as the electrospray ionization process or the sonic sprayionization process. The thus generated gaseous ion is then introducedinto a differential pumping portion 102 through a pore 101. The gaseousion is further introduced into a high vacuum portion 104 through a pore103, where the ion passes through an ion transport portion 105consisting of a multipole pole, for example, and is then introduced intoan ion trap 106. An RF voltage is supplied to the ion trap 106 from anRF power supply such that the gaseous ion is trapped at the center ofthe ion trap 106 by a quadrupole electric field. With regard tonon-analysis target ions, an RF voltage may be applied to the multipolepole in the ion transport portion so that the non-analysis target ionscan be removed in the ion transport portion 105.

In the case where no multipole pole is used in the ion transport portion105, the non-analysis target ions are removed in the ion trap 106, andan RF voltage for trapping the analysis target ions is applied to theion trap 106. The gaseous ion that has been trapped for a certainduration of time is transported to the right by an electric force andintroduced into an ion acceleration portion 108 of the time-of-flightmass spectrometer 107. In the ion acceleration portion 108, a pulsed RFvoltage is applied to the introduced gaseous ion at a specific time tothereby accelerate the gaseous ion until it has a certain kineticenergy. The thus accelerated gaseous ion has its trajectory altered by areflector 109 and thus its energy converged, before it is detected by adetector 110. The length of the ion trajectory between the ionacceleration portion 108 and the detector 110 is constant. Since the ionvelocity decreases with increasing m/z (mass/charge number) of the ion,the detector 110 detects ions in the order of increasing m/z values. Theoutput of the detector 110 is led to the information processing unitwhere the m/z of the ion is determined based on the ion detection time.Based on the thus obtained result of the primary mass spectroscopy, thepriority order of the ions as the target of the secondary massspectroscopy is determined in the information processing unit. Then, inorder to apply an RF voltage to the ion trap 106 for isolating only thetarget ions for the secondary mass spectroscopy from the ions introducedinto the ion trap 106, an instruction is sent from the informationprocessing unit to the RF power supply. Further, an instruction fordissociating the isolated ions by CID, for example, is sent from theinformation processing unit to the RF power supply, so that dissociatedfragment ions are produced in the ion trap 106. The fragment ions aretransported to the right by an electric force and introduced into theion acceleration portion 108 of the time-of-flight mass spectrometer107. In the ion acceleration portion 108, a pulsed RF voltage is appliedto the introduced gaseous ion at a specific time to thereby acceleratethe gaseous ion until it has a specific kinetic energy. The thusaccelerated gaseous ion has its trajectory altered by the reflector 109and is then detected by the detector 110. The output of the detector 110is delivered to the information processing unit where the m/z of the ionis determined based on the ion detection time. The secondary massspectroscopy is thus realized. A certain number of the secondary massspectroscopy target ions that have been prioritized are sequentiallysubjected to the secondary mass spectroscopy in accordance with thepriority order.

In the ion trap 106, a linear trap consisting of a quadrupole pole asshown in FIG. 51 may be used instead of the quadrupole ion trap. Thelinear trap (quadrupole) time-of-flight mass spectrometer per se isdescribed in Rapid Communications in Mass Spectrometry, Vol. 12 (1998)pp. 1463-1474, for example. The present embodiment is substantiallyequivalent to the quadrupole ion trap shown in FIG. 2 in terms offunctionality, but it is characterized in that the amount of ions thatcan be trapped at one time can be increased. To the linear trap, an RFvoltage is applied such that non-analysis target ions are removed andanalysis target ions can be trapped.

Alternatively, the mass spectrometer may only comprise the quadrupoleion trap spectrometer as shown in FIG. 52. A sample solution separatedin a liquid separation portion such as a liquid chromatograph isintroduced into an ion source where it is turned into a gaseous ion. Thethus produced gaseous ion is introduced into a differential pumpingportion 102 through a pore 101. The gaseous ion further passes through apore 103 and an ion transport portion 105 disposed in a high vacuumportion 104 and is then introduced into an ion trap 106. An RF voltageis supplied form an RF power supply to the ion trap 106 such that thegaseous ion is trapped at the center of the ion trap 106. To the iontrap 106, an RF voltage is applied such that non-analysis target ionsare removed and analysis target ions can be trapped.

The gaseous ion that has been trapped for a certain duration of time isdischarged from the ion trap 6 in accordance with the m/z of the ion asthe RF voltage applied thereto is continuously changed, and is thendetected by a detector 110. The output of the detector 110 is led to theinformation processing unit where the m/z of the ion can be determined(i.e., subjected to the primary mass spectroscopy) based on the iondetection time. As in the example of FIG. 47, the secondary massspectroscopy may also be performed. As compared with the time-of-flightmass spectrometer, although the quadrupole ion trap has a narrower rangeof mass spectroscopy and lower mass resolution and mass accuracy, itallows the apparatus to be reduced in size and also allows highlysensitive analysis to be performed.

In the embodiments shown in FIGS. 50, 51 and 52, by applying an RFvoltage in response to an instruction from the information processingunit, non-analysis target ions are eliminated prior to the primary massspectroscopy, so that the minute component that is desired to beanalyzed can be reliably subjected to mass spectroscopy. In particular,when the linear trap shown in FIG. 51 is employed, since the linear traphas a volume that is larger than that of the quadrupole ion trap shownin FIG. 47, for example, by two orders of magnitude, the minutecomponents can be more reliably subjected to mass spectroscopy.

The screen operations illustrated in FIG. 46 are carried out using thedisplay unit and the input unit. On the input screen displayed on thedisplay unit, the information about the analysis target ions (such asthe mass and the m/z of the ion) can be entered via the input unit priorto analysis. The first database is created as described above and storedby the storage means. Based on the first database, the RF power supplyis controlled in the information processing unit and an RF voltage isapplied to the ion trap 106 or the multipole pole in the ion transportportion 105. As a result, the RF voltage, for the purpose of resonancedischarge, is applied to those ions among the ions introduced to the iontrap 106 from the ion source that are other than the analysis targetions, and the analysis target ions are trapped by the ion trap 106. Ifthe ions that could possibly disrupt the analysis are known, theinformation about such ions may be stored in the second database. By sodoing, the non-analysis target ions can be removed by an RF electricfield for resonance discharge, while trapping the analysis target ionsin the ion trap 106. By these operations, in the event that any analysistarget ions contained in the ions produced by the ion source can betrapped by the ion trap 106 and then subjected to mass spectroscopy(primary mass spectroscopy). The information about the ions detected bythe primary mass spectroscopy is then collated with the first database,and the corresponding ions are preferentially subjected to tandem massspectroscopy (secondary mass spectroscopy). The priority order for thetandem mass spectroscopy may be descending order of ion intensity, or itmay start from the multivalent ions from which it is easier to detectfragment ions. Thereafter, the secondary mass spectroscopy target ions(of a single type) are isolated by the ion trap 6 in accordance with thepriority order and are then fragmented (dissociated) by CID, forexample. In the embodiments shown in FIGS. 50 and 51, the produced ions(fragment ions) are transported to the right by an electric force andthen subjected to analysis in the time-of-flight mass spectrometer 107.In the embodiment shown in FIG. 52, the secondary mass spectroscopy isconducted in the ion trap 106. Such a tandem mass spectroscopy (MS/MS)sequence is carried out on the analysis target ion one after another,thereby obtaining an MS/MS spectrum for each. Further, it is alsopossible to perform a higher-order tandem mass spectroscopy (MS^(n)(n=3, 4, . . .)) by similar operations.

FIG. 53 schematically illustrates the trapping of ions in a ion trap. Asshown in FIG. 53( a), normally an RF voltage for trapping the injectedions is applied to the ion trap, so that a mixture of the A⁺ and B⁺ ionsintroduced from the left is trapped by the ion trap in accordance withtheir abundance ratios. For example, when the abundance ratio of A⁺ ionsis far greater than that of B⁺ ions, there would be far more A⁺ ionsthat are trapped. Meanwhile, the total amount of ions that are trappedby the ion trap is limited by the space-charge effect. As a result, thenumber of B⁺ ions that are trapped can sometimes be only several, makingB⁺ ions difficult to detect. If there are several kinds of ions withhigh abundance ratios, such as A⁺ ions, at the same time, only thoseions with high abundance ratios could be dissociated by the ion trap andsubjected to CID, and the ions with lower abundance ratios, such as B⁺ions, might not be chosen as the target for tandem mass spectroscopy. Inthe case where another RF voltage for resonance-discharging A⁺ ions isapplied in a superposed manner in addition to the RF voltage fortrapping the injected ions in the ion trap, although A⁺ ions are onceintroduced into the ion trap, as shown in FIG. 53( b), they are heatedand then discharged from the ion trap to the outside. As a result, B⁺ions are concentrated in the ion trap and so the number of B⁺ ions thatcan be detected can be increased. This means that the B⁺ ion detectionsensitivity increases and B⁺ ions can also be subjected to tandem massspectroscopy. By applying an RF voltage to the ion transport portion 105for resonance-discharging A⁺ ions in a superposed manner in addition tothe RF voltage for trapping the injected ions, as shown in FIGS. 50, 51and 52, the direct introduction of A⁺ ions to the ion trap can beprevented. As a result, the detection sensitivity for B⁺ ions can befurther improved. In the embodiments of the invention, an improvement of2 to 3 folds was observed in the detection sensitivity for ions withlower ion abundance ratios due to the application of the RF voltage.

FIGS. 54, 55 and 56 show diagrams of apparatuses in which MALDI(matrix-assisted laser desorption ionization) is employed in the ionsource according to an embodiment. The example shown in FIG. 54 employsa quadrupole ion trap mass spectrometer, and the example shown in FIG.55 employs a quadrupole ion trap time-of-flight mass spectrometer. Theion trap 106 may adopt a quadrupole linear trap as shown in FIG. 56,instead of the quadrupole ion trap. A sample is fixed on a plate 111,together with a matrix substance, and dried. The thus prepared plate 111is placed inside the vacuum apparatus and is irradiated with a pulsedlaser. The vacuum apparatus has a window 112 through which a laser beamemitted by a laser that is oscillated under atmospheric pressure can beirradiated into the vacuum apparatus. As the plate 111 is irradiatedwith the laser beam (with a beam diameter of approximately 0.1 mm), ionsare produced within a time interval of the order of microseconds. Bymoving the location on the plate 111 that is irradiated with the laser,gaseous ions are produced in a consecutive manner. The thus producedions pass through the ion transport portion 105 consisting of amultipole pole, for example, and are introduced into the ion trap 106.An RF voltage is applied to the ion trap 106 such that the gaseous ionsare trapped at the center of the ion trap 106. Although in the presentembodiments the plate 111 is disposed within the vacuum apparatus, itmay alternatively be disposed under atmospheric pressure. In theembodiments shown in FIGS. 54, 55 and 56 too, non-analysis target ionscan be eliminated prior to the primary mass spectroscopy by applying anRF voltage in response to an instruction from the information processingunit, so that a minute component that is desired to be analyzed can bereliably subjected to mass spectroscopy.

FIG. 57 shows a diagram of an apparatus according to another embodimentof the mass spectroscopy system of the invention. The present embodimentinvolves a two-dimensional liquid chromatography/mass spectroscopysystem. A liquid sample is introduced into a liquid chromatograph column(LC column) in a first dimension via an injection valve. In order tocreate a gradient in a mobile-phase solution, two kinds of mobile-phasesolutions prepared in two liquid reservoirs 101 are introduced into theinjection valve while their flow volumes are adjusted by two pumps 101.The liquid sample separated in the LC column is sequentially introducedinto a switching valve 113 and adsorbed by a trap column. Afteradsorption is performed in the top column for a certain duration oftime, the pumps 101 are deactivated.

Then, the two kinds of mobile-phase solutions prepared in another twoliquid reservoirs 102 are introduced into the trap column with theirflow volume being adjusted by two pumps 102. A separated sample adsorbedon the trap column is eluted and introduced into a second liquidchomatography (LC) column where it is further separated. The separatedsamples are consecutively introduced into the mass spectrometer andsubjected to mass spectroscopy therein. After separation, the pumps 102are deactivated, and the pump 1 is activated. The liquid samples thatare separated in the first-dimension LC column are adsorbed by the trapcolumn for a certain duration of time, separated in the second-dimensionLC column, and then subjected to mass spectroscopy. Thus, the liquidsamples that have been two dimensionally LC-separated are consecutivelysubjected to mass spectroscopy. If the number of types of samples thatare mixed is small, the separation can be sufficiently carried out bythe LC/MC analysis alone that utilizes only one-dimensional LC. However,when there are great many kinds of samples, even the two-dimensional LCmay not be capable of achieving complete separation, often resulting ina mixture of samples being introduced for MS. As mentioned above, thereis a limit to the number of kinds of ions that can be subjected totandem mass spectroscopy in an identical sample. Thus, it is veryeffective to preferentially subject the analysis target substances totandem mass spectroscopy in the case of a minute sample.

In cases where the analysis target substances are clearly identified andthe number of analysis samples is large, a high-throughput analysis canbe performed by using the LC columns in parallel. In the embodimentshown in FIG. 58, where the LC/MS analysis is performed, LC and the ionsources are used in parallel. If the LC elation time of the analysistarget substance can be predicted, the time when a gaseous ion derivedfrom the analysis target substance is generated can be shifted byshifting the start time of the LC analysis. Namely, after the analysisof the gaseous ion derived from the analysis target substance that isproduced from the ion source 101, the gaseous ion derived from theanalysis target substance that is produced from the ion source 102 isanalyzed. At the coupling portion between the ion source and the massspectrometer, a plurality of ion sources are temporally switched. Theion sources and the LC columns may be integrated. In another method, asingle ion source may be employed, and the separated liquid samples thatare introduced into the ion source may be switched by a valve, forexample. In this case, however, the distance between the end of LC andthe ion source would be too long, and the degree of separation might bereduced upon generation of ions. In this type of parallel LC process,the wait period (approximately 1 hour) in which the gaseous ion derivedfrom the analysis target substance is not analyzed can be effectivelyutilized, thereby enabling a high-throughput analysis. Although in thepresent embodiment the number of parallel processes is two, the numbermay be increased. In order to allow a plurality of types of substancesto be analyzed, the correspondence between the movement time of the ionsource and the analysis target ions listed in the first database and thestart time of the LC analysis, for example, can be usefully specified inadvance via the input unit.

In the evaluation of metabolites and diagnosis, the analysis targetsubstance is clearly identified in advance, and the substance must bequantified. In such a case, by adding a certain amount of an internalstandard substance that has substantially identical chemical propertiesto those of the analysis target substance and that differs only inmolecular amount to the sample, the quantitative analysis can beaccurately performed. In a typical internal standard substance, stableisotopes such as deuterium, ¹³C, ¹⁸O, and ¹⁵N are substituted. In theinternal standard substance, the elation time in the separation meanssuch as LC is the same, the chemical properties such as the loss due toadsorption on the wall surface and the ionization efficiency in the ionsource are the same, but the mass number is different. In the result ofthe primary mass spectroscopy (mass spectrum) obtained from such asample, a pair of peaks are detected, as shown in FIG. 59. A peakindicated by reference A is the peak of the analysis target substance,and a peak referenced by B is the peak of the substance in whichisotopes are substituted. As there is the possibility that ions derivedfrom different substances with the same mass are superposed by chance,the two peaks are separately subjected to tandem mass spectroscopy.Then, based on the result of the secondary mass spectroscopy (MS/MSspectrum), the analysis target substance is identified. Quantitativedetermination may be further conducted based on a ratio of the ionintensities (peak areas). When such a quantitative determination isconducted, the pair of the analysis target ions must be registered in alist in the first database in advance. The figure also shows severalpeaks in addition to those referenced by arrows. Even if all of suchpeaks correspond to the peaks registered in the list in the firstdatabase, the pair of peaks indicated by the arrows must bepreferentially selected as the targets for tandem mass spectroscopy.Further, if the peak of only one of the pair is detected, the ionsshould be regarded as having not detected and do not need to be selectedas the targets for tandem mass spectroscopy even when the ions areregistered in the list in the first database. These analysis results aredisplayed in terms of concentration or relative ratios (%, for example)together with the sample number. In the case of diagnosis, for example,the range of normal or abnormal values is predetermined. Thus, when theanalysis result exceeds an expected range, the excess is represented byan indication (by way of color, underlining, asterisk, or font, forexample) in the output result displayed on the screen, in a printout, orin an electronic mail, for ease of recognition.

In the following, various examples of the invention are listed:

-   (1) In a mass spectroscopy system using a tandem mass spectrometer    in which a substance to be the target of measurement of the mass    spectrometer is ionized, an ion species with a specific    mass-to-charge-ratio m/z is selected from a variety of ion species    that are produced, the specific ion species is dissociated, wherein    the selection, dissociation, and measurement of the ion species as    the measurement target are repeated in multiple stages. The    selection and dissociation of ion species are repeated n−1 times    (where n is an integer ≧1) and are then subjected to mass    spectroscopy. Based on the result of an n-stage mass spectroscopy    (MS^(n)), which is a measured mass spectrum represented in terms of    a peak of a measured intensity against the mass-to-charge-ratio m/z    of an ion, it is determined whether or not there is the possibility    of correspondence to characteristics data (such as the mass number m    of an ion species and/or the retention time τ in a liquid    chromatography unit and/or a gas chromatography unit if one or both    of these are provided in a stage prior to the mass spectrometer) for    an ion species that is designated in advance. Based on this    determination, the content of the next MS^(n) analysis is    automatically determined within a specific duration of time.-   (2) The characteristics data about the ion species designated in    advance is stored in a database the mass spectroscopy system    possesses internally.-   (3) The database the mass spectroscopy system possesses internally    automatically stores the characteristics data about the ion species    that has been once measured, or the characteristics data about a    variety of peptides of which the breakdown or production by a    designated enzyme is predicted for a protein that has been once    identified.-   (4) The database the mass spectroscopy system possesses internally    stores the characteristics data about a variety of peptides of which    the breakdown or production by a designated enzyme is predicted for    a protein entered or designated in advance by a user.-   (5) The database the mass spectroscopy system possesses internally    stores the characteristics data about a specific ion species derived    from noise or impurity that is entered or designated by the user in    advance.-   (6) The database the mass spectroscopy system possesses internally    stores, even during measurement, the data that has already been    measured as needed.-   (7) In a method of automatically determining the content of the next    MS^(n) analysis within a certain period of time based on the result    of a determination as to the possibility of correspondence to the    characteristics data about an ion species that is designated in    advance, a mass spectrum that is the result of an n-stage mass    spectroscopy (MS^(n)) is represented in terms of a peak (ion peak)    of a measured intensity against the mass-to-charge-ratio m/z of an    ion. An ion peak with a certain m/z value that is determined to    correspond to the characteristics data is selected as the target ion    species for the selection and dissociation in the next MS^(n)    analysis if the next MS^(n) analysis is MS^(n) (n≧2), or avoided    from becoming the target.-   (8) In a method where, when the next MS^(n) analysis is MS^(n)    (n≧2), the ion peak with the certain m/z value that has been    determined to correspond to the characteristics data is avoided from    becoming the target ion species for the selection and dissociation    in the next MS^(n) analysis, the peaks that have been determined to    not correspond to the characteristics data are selected as the    target ion species for the next MS^(n) analysis in the order of    decreasing intensity.-   (9) In a method of automatically determining the content of the next    MS^(n) analysis within a specific period of time, the specific    period of time refers to the time between an n-stage mass spectrum    measurement (MS^(n)) and the time that does not interrupt the next    analysis measurement, a preparation time when transitioning from an    n-stage mass spectrum measurement (MS^(n)) to the next analysis, or    any of the times of 100 msec, 10 msec, 5 msec, and 1 msec.-   (10) In a method of automatically determining the content of the    next MS^(n) analysis within a specific time period, the next MS^(n)    analysis refers to the selection of an ion peak with a certain m/z    value from an n-stage mass spectrum (MS^(n)), an n-th stage    dissociation, and an n+1th stage mass spectroscopy (MS^(n+1)).-   (11) In a method of automatically determining the next MS^(n)    analysis content within a specific period of time, the next MS^(n)    analysis content comprises selecting an ion peak, upon obtaining the    result of an n-th stage mass spectroscopy (MS^(n)), from the result    of an n−1-th mass spectroscopy (MS^(n−1)) that has an m/z value that    is different from the certain m/z value of the ion peak selected in    the n−1-th mass spectrum (MS^(n−1)), dissociating the ion peak, and    then performing the n-th mass spectroscopy (MS^(n)) again.-   (12) In a method in which the ion peak with a different m/z value    from the certain m/z value of the ion peak that has been selected in    the n−1-th stage mass spectrum (MS^(n−1)) is selected, upon    obtaining the result of the n-th stage mass spectroscopy (MS^(n)),    from the result of the n−1-th mass spectroscopy (MS^(n−1)) and then    dissociated, and the n-th stage mass spectroscopy (MS^(n)) is    performed again, upon obtaining the result of the n-th stage mass    spectroscopy (MS^(n)), an ion peak with the same mass number m and a    different valence z from the ion peak with the certain m/z value    that has been selected in the n−1-th mass spectrum (MS^(n−1)) is    selected from the result of the n−1-th mass spectroscopy (MS^(n−1))    and then dissociated, and the n-th stage mass spectroscopy (MS^(n))    is performed again.-   (13) In a method of automatically determining the next MS^(n)    analysis content within a specific period of time, the next MS^(n)    analysis content comprises performing the 1^(st)-stage mass    spectroscopy (MS¹) on a next sample, or terminating the measurement,    instead of proceeding to tandem mass spectroscopy where a    higher-stage dissociation and analysis is performed.-   (14) In a method of automatically determining the content of the    next MS^(n) analysis within a specific period of time, operating    conditions, such as the voltage in a tandem mass spectroscopy    apparatus, are automatically adjusted or changed depending on the    content of the next MS^(n) analysis.-   (15) In a method of changing the operating conditions, such as the    voltage in the tandem mass spectroscopy apparatus, depending on the    content of the next MS^(n) analysis, a mass spectroscopy system in    which, if the next MS^(n) analysis is MS^(n) (n≧2), the operating    conditions such as the voltage in the tandem mass spectroscopy    apparatus are automatically adjusted or changed depending on the    value of the mass-to-charge-ratio m/z of a parent ion that is the    target for selection and dissociation.-   (16) The characteristics data include the mass number, valence,    mass-to-charge-ratio or m/z value, and detection intensity of the    ion species, the retention time of liquid chromatography (LC) or gas    chromatography (GC), solvents for LC or GC or their mobile-phase    ratio, the flow volume or gradient of LC or GC, and, in cases where    a two-dimensional LC is used, a sample number of the sample that was    divided during the ion exchange in the one-dimensional LC. The    characteristics data also include, in cases where a MADLI ion source    is employed, the spot position, number or coordinates on a sample    plate, and the content of measures to be taken, in accordance with a    user specification, for example, for each of the ion species that    corresponded to the stored characteristics data (such as whether or    not a particular ion species should be excluded from the target ion    species for the next MS^(n) (n≧1) analysis, whether or not a    particular ion species should be selected as the target ion species    for the next MS^(n) (n≧1) analysis, or whether or not the particular    ion species should be removed upon or prior to the injection of an    ion sample into the mass spectroscopy system), analysis conditions    including the date of measurement, a column number of the LC or GC    used, an order n of the tandem mass spectroscopy MS^(n), and the    operating condition of the mass spectrometer, and, in cases    involving a protein or peptide sample, information about the    inferred structure of an ion species, such as the amino acid    sequence.-   (17) A mass spectroscopy system comprising a function for    automatically correcting or calibrating the retention time of    actually measured data concerning liquid chromatography (LC) or gas    chromatography (GC) based on a comparison of an actually measured    retention time of a designated reference substance and a retention    time of a reference substance stored in a database provided in the    system.-   (18) With regard to the mass number and the mass-to-charge ratio m/z    value of an ion species, if the ion species is accompanied by an    isotope peak upon deriving of the mass number, the mass number    without isotopes is obtained, and, with regard to the mass-to-charge    ratio m/z value, if the value fluctuates as time elapses from the    start of measurement, at least one reference substance with a known    m/z value is contained in the sample, and, in the case of a    plurality of reference substances, reference substances with    different retention times of LC or GC are selected, and by comparing    the m/z value of an actually measured reference substance and the    known m/z value, the m/z value that fluctuates with the lapse of    time from the start of measurement is automatically corrected or    calibrated.-   (19) The characteristics data of the ion species that is designated    in advance is the characteristics data of a peptide.-   (20) The characteristics data of the ion species that is designated    in advance is the characteristics data of a peptide derived from a    specific protein.-   (21) The characteristics data of the ion species that is designated    in advance is the characteristics data of a modifying structure such    as a specific sugar chain.-   (22) The characteristics data of the ion species that is designated    in advance is the characteristics data of a specific chemical    substance.-   (23) In a mass spectroscopy system in which the next MS^(n) analysis    content is automatically determined within a specific time period,    wherein the items that are entered by the user include the presence    or absence of the need for the determination of a digestive enzyme    or isotope peaks, the presence or absence of the need for collation    with an internal database or a search thereof, and the ion selection    resolution.-   (24) The characteristics data of the ion species that is designated    in advance is the characteristics data of a protein or peptide with    a modifying structure such as phosphorylation.-   (25) In a method of determining the presence or absence of the    possibility of correspondence to the characteristics data of an ion    species designated in advance, wherein the determination is made    within a tolerance or a certain range designated by the user, for    example.-   (26) In a method of automatically determining the content of the    next MS^(n) analysis within a certain time period by determining the    presence or absence of the possibility of correspondence to the    characteristics data of an ion species that is designated in    advance, and, based on the result of the determination, the content    of the next MS^(n) analysis determined by the present system, or, in    the case of MS^(n) (n≧2), the target ion species for selection or    dissociation, is displayed on a display or in a file.-   (27) In a method of displaying the next MS^(n) analysis content,    there is provided a user-dialog interface that allows the user to    acknowledge the next MS^(n) analysis content, for example, so that    the next MS^(n) analysis can be performed once such an    acknowledgement is obtained.-   (28) A mass spectroscopy system comprising a plurality of    information processing units that perform a process in a parallel    manner.-   (29) In a method of performing a parallel processing in a plurality    of information processing units, a single database is divided into a    plurality of databases that are allocated to a plurality of    information processing units, wherein a divided database search    process is carried out by each of the information processing units    in order to perform a database search in a parallel manner.-   (30) In a method of performing a parallel processing in a plurality    of information processing units, in the case where there are a    plurality of databases, each database is allocated to each of a    plurality of information processing units and a database search    process is carried out by each of the information processing units,    thereby performing a plurality of database searches in a parallel    manner.-   (31) In a mass spectroscopy system in which, with regard to the    result of mass spectrum measurement in the n-th stage mass    spectroscopy (MS^(n)), the presence or absence of the possibility of    correspondence to the characteristics data of an ion species    specified in advance is determined and, based on the result of the    determination, the next MS^(n) analysis content is automatically    determined within a specific period of time, in the case where a    liquid or gas chromatography unit is provided in a stage before a    mass spectrometer, a sample is passed through the liquid or gas    chromatography unit so that temporally separated samples due to the    difference in the retention time during the passage are subjected to    mass spectroscopy in a mass spectroscopy unit in a later stage,    wherein a measurement in which all of the samples are passed through    the liquid or gas chromatography unit and subjected to mass    spectroscopy is performed at least twice on the same sample, and    wherein the characteristics data of a parent ion with a high    intensity that has been subjected to an MS² analysis in a previous    measurement, the characteristics data being stored in an internal    database, is utilized in a second measurement and in any of the    subsequence measurements where low-intensity ions that are yet to be    measured are preferentially subjected to a MS² analysis.-   (32) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which a substance as a measurement target    for a mass spectrometer is ionized and, from a variety of resultant    ion species, an ion species with a specific mass-to-charge ratio m/z    is selected and dissociated, wherein the selection, dissociation,    and measurement of the ion species as the measurement target are    repeated in multiple stages, wherein the selection and dissociation    of an ion species are performed n−1 times and mass spectroscopy is    performed thereon to obtain an n-th stage mass spectroscopy (MS^(n))    result that is a measured mass spectrum represented in terms of a    peak of measurement intensity versus the mass-to-charge ratio m/z of    the ion, wherein, based on the measurement result, an isotope peak    is determined, on the basis of the result of which the next MS^(n)    analysis content is automatically determined within a certain period    of time.-   (33) In a method whereby an ion species is selected and dissociated    n−1 times and is then subjected to mass spectroscopy to obtain an    n-th stage mass spectrum measurement result (MS^(n)), based on which    the presence or absence of the possibility of correspondence to the    characteristics data of an ion species that is designated in advance    is determined, each of ion peaks with different m/z values in the    n-th stage mass spectrum measurement (MS^(n)) result is subjected to    an isotope peak determination, and an ion valence is derived from    the interval between the ion peak and a peak inferred to be an    isotope peak, the mass number m of each ion peak is calculated, and,    based on the result of the calculation, the next MS^(n) analysis    content is automatically determined within a certain period of time.-   (34) In a method of automatically determining the next MS^(n)    analysis content within a specific period of time based on the    result of determination of an isotope peak, of peaks with an ion    peak interval of not more than 1.1 Da, one with a larger    mass-to-charge ratio m/z is inferred to be an isotope peak, an ion    valence is derived from the interval between the peaks, the mass    number m of each ion peak is calculated, and, based on the value of    the mass number m, the next MS^(n) analysis content is automatically    determined within a certain period of time.-   (35) The ion valence and the mass numbers m of the ion peaks    calculated on the basis of the isotope peak determination are    displayed on a display or in a file.-   (36) In a method of automatically determining the next MS^(n)    analysis content within a certain time period based on the result of    determination of an isotope peak, it is determined whether or not a    particular peak estimated to be an isotope peak is an isotope peak    by calculating the intensity distribution of isotope peaks based on    the mass number m of each ion peak that is estimated by calculation,    and then by determining whether or not the particular peak    corresponds to the thus calculated intensity distribution precisely    or with an error of less than50%.-   (37) In a method of automatically determining the next MS^(n)    analysis content within a specific time period based on the result    of determination of an isotope peak, the intensity distribution of    isotope peaks is calculated in advance in accordance with the mass    number m of an ion, wherein the result of the calculation, namely a    distribution pattern of isotope peaks, is stored in a memory medium    such as a memory or a database, and then it is automatically    determined, within a specific time period, whether or not a    particular peak is an isotope peak based on whether or not the    distribution pattern of isotope peaks corresponding to the mass    number m of each ion peak that is estimated by calculation    corresponds to the distribution pattern of estimated isotope pattern    completely or with an error of less than 50%.-   (38) In a system for automatically determining the next MS^(n)    analysis content within a specific time period based on the result    of determination of an isotope peak, data such as the valence z and    the mass number m of each ion peak, or the element compositional    distribution inferred from the mass number, is displayed on a    display, outputted in a data file, or stored in the internal    database.-   (39) In a method of automatically determining the next MS^(n)    analysis content within a specific time period based on the result    of determination of an isotope peak, a mass spectroscopy system in    which, when selecting an ion peak as the target for the next MS^(n)    analysis, an isotope peak is selected or avoided, or a peak    containing no isotopes is selected.-   (40) In a method of automatically determining the next MS^(n)    analysis content within a specific time period based on the result    of determination of an isotope peak, when selecting an ion peak as a    selection and dissociation target for the next MS^(n) analysis, an    isotope peak is also selected.-   (41) In a method of automatically determining the next MS^(n)    analysis content within a specific time period based on the result    of determination of an isotope peak, when selecting an ion peak as a    selection and dissociation target for the next MS^(n) analysis, an    ion species with a valence of two or more is preferentially    selected.-   (42) In a method of automatically determining, within a specific    time period, whether or not a particular ion peak is an isotope    peak, whereby an intensity distribution of isotope peaks is    calculated in accordance with the mass number m of an ion in    advance, and the result of the calculation, i.e., a distribution    pattern of the isotope peaks, is stored in a memory medium such as a    memory or a database, wherein it is determined whether or not the    distribution pattern of the isotope peaks for the mass number m of    each ion that is estimated by calculation corresponds to the    distribution pattern of an estimated isotope peak completely or with    an error of less than 50%, a mass spectroscopy system in which, for    a plurality of ion species with very close mass-to-charge ratio m/z    values and different mass numbers m or valence z, the intensity    distribution of an isotope peak is calculated in advance in    accordance with the mass number m of each ion species, and the    result of the calculation, i.e., the distribution pattern of the    isotope peak is stored in a memory medium such as a memory or a    database, wherein it is determined whether or not the distribution    pattern corresponds to the distribution pattern of peaks in the    result of the n-th stage mass spectrum measurement (MS^(n))    completely or with an error of less than50% in order to    automatically determine, within a specific time period, whether or    not the peak contains a plurality of ion species.-   (43) In a mass spectroscopy system in which, for a plurality of ion    species with very close mass-to-charge ratio m/z values and    different mass numbers m or valence z, the intensity distribution of    an isotope peak is calculated in advance in accordance with the mass    number m of each ion species, and the result of the calculation,    i.e., the distribution pattern of the isotope peak is stored in a    memory medium such as a memory or a database, wherein it is    determined whether or not the distribution pattern corresponds to    the distribution pattern of peaks in the result of the n-th stage    mass spectrum measurement (MS^(n)) completely or with an error of    less than 50% in order to automatically determine, within a specific    time period, whether or not the peak contains a plurality of ion    species, a peak that is determined to contain a plurality of ion    species is avoided or selected as the target for the next MS^(n)    analysis.-   (44) In a system in which a peak that is determined to contain a    plurality of ion species is selected as the target for the next    MS^(n) analysis, the possibility of the presence of a plurality of    ions is displayed, and the information that is obtained upon    determination of the presence of a plurality of ion species, such as    the mass number m and valence z of the multiple ion species, is used    in the analysis of the data obtained as a result of the next MS^(n)    analysis.-   (45) The characteristics data of an ion species that is designated    in advance is the characteristics data of an ion derived from a    sample that is labeled by an isotope in the case where, in a    pre-processing stage prior to mass spectroscopy, there are samples    that are labeled by an isotope and samples that are not labeled by    an isotope.-   (46) In a method of determining the presence or absence of the    possibility of correspondence between the characteristics data of an    ion species that is designated in advance and the result of an n-th    stage mass spectrum measurement (MS^(n)) that is obtained by    performing the selection and dissociation of ion species n−1 times    and then subjecting the ion species to mass spectroscopy, it is    determined whether or not the mass-to-charge ratio m/z value of each    ion peak in the result of the n-th stage mass spectrum measurement    (MS^(n)) corresponds to the m/z value calculated from the mass    number m of the ion species designated in advance and from a valence    within an assumed range (1≦z≦Nz).-   (47) In a method of automatically determining the next MS^(n)    analysis content within a certain period of time, the MS^(n)    spectrum data is analyzed and it is then determined whether or not    each mass peak obtained during the certain time period is noise,    wherein a peak that is determined to be noise is automatically    eliminated.-   (48) In a method of automatically determining the next MS^(n)    analysis content within a certain time period, of the ion peaks in    the result of the n-th stage mass spectroscopy (MS^(n)), an ion peak    of which the intensity varies by more than50% at each measurement    time is avoided or selected as the target ion species for the    selection or dissociation in the next MS^(n) analysis.-   (49) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, the mass spectrometer comprises an ion trap mass    spectrometer.-   (50) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, the mass spectrometer comprises an ion trap    time-of-flight mass spectrometer.-   (51) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, the mass spectrometer comprises a linear trap    time-of-flight mass spectrometer.-   (52) In an ion trap, or in the linear trap according to claim 33,    when the next MS^(n) analysis content is MS^(n) (n≧2), an RF voltage    (frequency or voltage) applied to the ion trap or linear trap during    the trap isolation of a target ion species is automatically adjusted    or changed in accordance with the mass-to-charge ratio m/z or the    selection and dissociation target ion species.-   (53) In an ion trap or the linear trap according to claim 33, when    the next MS^(n) analysis content is MS^(n) (n≧2), if the    dissociation target ion species is to be dissociated by the    collision induced dissociation (CID) described in claim 37, an    auxiliary AC (frequency or voltage) for collision induced    dissociation that is applied in a superposed manner in addition to    the RF voltage applied to the ion trap or linear trap during the    trap isolation of the target ion species is automatically adjusted    or changed in accordance with the mass-to-charge ratio m/z of the    dissociated target ion species.-   (54) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, the mass spectrometer comprises a    Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer.-   (55) A parallel computer is employed for the calculation process in    a mass spectroscopy system for automatically determining the next    MS^(n) analysis content within a specific period of time.-   (56) A cache memory or a hard disc is employed for the storage of    necessary data for the calculation process in a mass spectroscopy    system for automatically determining the next MS^(n) analysis    content within a specific period of time.-   (57) In a method of employing a memory or a hard disc for the    storage of necessary data, such as the stored data in an internal    database, for the calculation process in a mass spectroscopy system    for automatically determining the next MS^(n) analysis content    within a specific period of time, the necessary data in the hard    disc is written in the memory at certain time intervals determined    by a user, for example, wherein the memory is accessible at all    times during mass spectroscopy measurement so that the data on the    memory can be utilized and then stored.-   (58) In a method of employing a memory or a hard disc for the    storage of necessary data, such as the stored data in an internal    database, for the calculation process in a mass spectroscopy system    for automatically determining the next MS^(n) analysis content    within a specific period of time, the necessary data in the hard    disc is written in the memory at the start of mass spectroscopy    measurement, wherein the memory is accessible at all times during    mass spectroscopy measurement so that the data on the memory can be    utilized for analysis and then stored, wherein the necessary data on    the memory is written on the hard disc at the end of mass    spectroscopy measurement.-   (59) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, collision induced dissociation (CID) or electron    capture detection (ECD) as a method of dissociating an ion species.-   (60) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, of the ion peaks in the result of the n-th stage    mass spectroscopy (MS^(n)), an ion peak with an intensity ratio of    less than 70% relative to a peak with a maximum intensity is    selected or avoided as the target ion species for selection and    dissociation in the next MS^(n) analysis.-   (61) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, of the ion peaks in the result of the n-th stage    mass spectroscopy (MS^(n)), an ion species that is repeatedly    detected for more than a certain period specified by a user, for    example, is selected as the target ion species for the selection and    dissociation in the next MS^(n) analysis, or is determined to be a    noise peak due to impurity and avoided from being selected as the    target ion species for the selection and dissociation in the next    MS^(n) analysis.-   (62) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which the selection, dissociation, and    measurement of an ion species as a measurement object are repeated    in multiple stages, of the ion peaks in the result of the n-th stage    mass spectroscopy (MS^(n)), an ion species that is repeatedly    detected within a certain period specified by a user, for example,    is selected as the target ion species for the selection and    dissociation in the next MS^(n) analysis, or is determined to be a    noise peak due to impurity and avoided from being selected as the    target ion species for the selection and dissociation in the next    MS^(n) analysis.-   (63) An ion species that is repeatedly detected within a certain    time period specified by a user, for example, is subjected to the    MS^(n+1) analysis, which is the next MS^(n) analysis, as the target    ion species for selection and dissociation an indefinite number of    times as long as the analysis is performed within the certain time    period specified by the user, for example, even if the ion species    corresponds to data stored in an internal database in terms of    retention time and other data within a certain tolerance, wherein    the MS^(n+1) analysis data obtained within the certain time period    in which the same ion species has been used as the target ion    species for selection and dissociation is accumulated during or    after measurement.-   (64) The information about the ion species that has been subjected    to the MS^(n) (n≧2) analysis and the measurement information and    conditions are automatically stored in an internal database of a    mass spectroscopy system as a data set with a registration number    allocated thereto.-   (65) The information about the ion species that has been subjected    to the MS^(n) (n≧2) analysis and the measurement information and    conditions include the mass number m of the ion, valence z, ion    intensity, the retention time in liquid or gas chromatography, and,    in the case where there is provided a means for storing ions, the    accumulation time of the ion species.-   (66) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information and conditions in an internal database of a    mass spectroscopy system with a registration number allocated    thereto, by specifying the registration number or a condition of    data in a data set, actual-measurement mass spectrum data    corresponding to a data set that contains data that satisfies the    registration number or the data condition is referenced, displayed,    or outputted in a file.-   (67) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information and conditions in an internal database of a    mass spectroscopy system with a registration number allocated    thereto, the measured mass spectrum data is automatically evaluated    or analyzed, and an evaluation indicator obtained as a result is    automatically stored in the database.-   (68) In a method of automatically evaluating or analyzing the    measured mass spectrum data and automatically storing the result,    i.e., an evaluation indicator, in a database, the reliability and    quality of the measured spectrum data are evaluated.-   (69) The evaluation indicator of the measured mass spectrum data    indicates the temporal displacement between the time of measurement    of a measurement object and the time at which the detection    intensity of an ion eluted from the measurement object during liquid    or gas chromatography exhibits a peak, or the S/N ratio.-   (70) In a method of automatically evaluating or analyzing the    measured mass spectrum data and automatically storing the result,    i.e., an evaluation indicator, in a database, in the case where the    measurement object is a peptide, the number of amino acids that have    been read as a result of the analysis of the MS² spectrum data, the    reasons for the determination, and the result of decoding of the    amino acids are stored in the database.-   (71) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information and conditions in an internal database of a    mass spectroscopy system with a registration number allocated    thereto, if there are a plurality of data sets (ion species,    measurement information and measurement conditions) registered in    the database, in which the data obtained in the MS¹ analysis stored,    that are determined to be identical within a certain tolerance, the    redundant data sets are automatically deleted from the database or    added together.-   (72) The tolerance within which particular data sets are evaluated    to be identical, and the information such as valence, mass number    and retention time are specified by the user.-   (73) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information and conditions in an internal database of a    mass spectroscopy system with a registration number allocated    thereto, a system in which, if there are a plurality of data sets    that contain ion species information that is determined to belong to    an identical ion, the data sets that contain redundant ion species    information are automatically deleted from the database.-   (74) In a method whereby, if there are a plurality of data sets that    contain ion species information that is determined to belong to an    identical ion, the data sets that contain redundant ion species    information are automatically deleted from an internal database of a    mass spectroscopy system, the mass spectrum data corresponding to    the data sets that contain redundant ion species information is    automatically deleted or added.-   (75) In a method of determining identical ions based on the    information about ion species stored in a database, identical ions    refer to those ions of which the mass numbers, valence, and the    retention time in liquid or gas chromatography correspond within a    certain tolerance.-   (76) When performing the next MS^(n) analysis (n≧2) in which an ion    species with the same mass number and a different valence from the    target ion species (parent ion) for selection and dissociation in    the MS^(n) analysis that has already been measured is used as the    target ion species for selection and dissociation, the MSn (n≧2)    spectrum data obtained by using the ion species with the same mass    number and a different valence as the selection and dissociation    target ion species is fused with or added to the MS^(n) spectrum    data that has already been measured.-   (77) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information in the internal database of a mass    spectroscopy system with a registration number allocated thereto, in    the case where an MS^(n) (n≧3) analysis has been conducted, the mass    spectrum data obtained by conducting an MS² analysis of an ion    species that contains the precursor ion in the structure thereof    that has been used as the object of analysis in the MS^(n) (n≧3)    analysis is added with the mass spectrum data obtained by conducting    the MS^(n) (n≧3) analysis, and the thus combined data is stored in    the database with a registration number allocated thereto.-   (78) In a method of storing the information about the ion species    that has been subjected to the MS^(n) (n≧2) analysis and the    measurement information in the internal database of a mass    spectroscopy system with a registration number allocated thereto, in    the case where there is mass spectrum data obtained by conducting an    MS² analysis on the same substance using different dissociation    methods, the multiple items of mass spectrum data are added and then    stored in the database with a registration number allocated thereto.-   (79) The different dissociation methods include collision induced    dissociation (CID) and electron capture dissociation (ECD).-   (80) In a method of adding a plurality of items of mass spectrum    data, the ratio of each item of mass spectrum data can be designated    by the user.-   (81) If it is estimated that, as a result of an analysis of the    MS^(n) spectrum data obtained by using a protein or peptide as the    analysis object, a modifying structure such as phosphorylation is    added, information about the type of the estimated modifying    structure and the location where the modifying structure is added    (to which amino acid of the amino acid sequence the structure is    added) is also stored in the internal database of the mass    spectroscopy system.-   (82) The internal database of a mass spectroscopy system stores a    peptide sequence or the mass number of the peptide sequence that is    produced upon enzymatic digestion of all or some of the proteins    stored in databases, such as those that are made public, of the    amino acid sequences of general proteins, using a variety of    enzymes, wherein it is determined whether or not a particular ion    peak in the mass spectrum data of MS¹ has any possibility of    corresponding to the data stored in the internal database, and the    next MS^(n) analysis content is automatically determined within a    specific time period based on the result of the determination.-   (83) The presence or absence of the possibility of a particular ion    peak in the MS¹ mass spectrum data corresponding to any data stored    in the database about the enzymatically digested peptide sequence or    the mass number thereof, wherein an ion species that corresponds or    does not correspond within a certain tolerance is selected as the    selection and dissociation target ion species (parent ion) for the    MS² analysis, and the content of the next MS^(n) analysis is    automatically determined within a certain time period.-   (84) In a method of referring to, displaying, or outputting in a    file actually measured mass spectrum data for a data set containing    data in the internal database of a mass spectroscopy system that    satisfies a specified registration number or data condition, isotope    peaks are removed from the actually measured mass spectrum data, and    ion peaks with various valence values are converted such that they    are monovalent.-   (85) In a method of referring to, displaying, or outputting in a    file actually measured mass spectrum data for a data set containing    data in the internal database of a mass spectroscopy system that    satisfies a specified registration number or data condition, the ion    intensity of a peak that is determined to be an isotope peak is    added to the intensity of a monoisotopic peak.-   (86) In a mass spectroscopy system employing a tandem mass    spectroscopy apparatus in which a measurement object substance for a    mass spectrometer is ionized, an ion species with a specific    mass-to-charge ratio m/z is selected and dissociated from a variety    of ion species that are produced, and the selection, dissociation,    and measurement of the ion species as a measurement object are    repeated in multiple stages, the selection and dissociation of an    ion species is performed n−1 times (n≧2), and the result of an n-th    stage mass spectroscopy (MS^(n)) in which the selected and    dissociated ion species is subjected to mass spectroscopy, namely    mass spectrum data represented in terms of a peak of measurement    intensity against the mass-to-charge ratio m/z of the ion, is    analyzed within the real time of measurement, wherein the next    MS^(n) analysis content is automatically determined within a    specific time period based on the result of the analysis.-   (87) The substance as the measurement object for the mass    spectrometer is a protein, peptide, or a peptide with a modifying    structure.-   (88) The substance as the measurement object of the mass    spectrometer is a modifying structure such as a sugar chain, or a    compound with a modifying structure.-   (89) The substance as the measurement object of the mass    spectrometer is a substance consisting of a limited number of types    of basic structural units that are linked.-   (90) In the analysis performed on the result of an n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum data represented in    terms of a peak of measurement intensity against the mass-to-charge    ratio m/z of the ion, the structural unit making up the parent ion,    such as an amino acid, amino acid with a modifying structure, or a    sugar chain, or a structure consisting of several linked structural    units, is estimated from a mass peak interval, mass-to-charge ratio    m/z, and an intensity distribution in the mass spectrum data within    a specific time period.-   (91) When estimating the structural unit of the parent ion within a    specific time period, when the substance as the measurement object    for the mass spectrometer is a peptide or a peptide with a modifying    structure, an amino acid or a structure consisting of several amino    acids is estimated from the mass peak interval of the mass spectrum    data.-   (92) When estimating a relevant amino acid from the mass peak    interval in the mass spectrum data, a dissociated amino acid is    estimated from both the N and C terminals of a peptide consisting of    amino acids.-   (93) When estimating a relevant amino acid from the mass peak    interval in the mass spectrum data, the number of amino acids that    are estimated with an accuracy or a score of more than a certain    value is derived.-   (94) If the number of the amino acids that are estimated with an    accuracy or score exceeding a certain value as a result of the    analysis of the n-th stage mass spectroscopy (MS^(n)) mass spectrum    data (n≧2) exceeds a certain number designated by the user, for    example, the next MS¹ analysis measurement is conducted or    terminated, and if the number is less than the certain designated    number, the MS^(n+1) analysis in which one of the ion species that    have been detected in the MS^(n) data (n≧2) is selected and    dissociated and then subjected to mass spectroscopy is automatically    conducted, or, if an ion species with a substantially identical mass    number to that of the parent ion in the MS^(n) analysis and with a    different valence has been detected in the MS^(n−1) data, the ion    species is selected and dissociated and the MS^(n) analysis is    automatically conducted again.-   (95) When conducting the MS^(n+1) analysis in which one of the ion    species detected in the MS^(n) data (n≧2) is selected, dissociated    and subjected to mass spectroscopy in the event that the number of    the amino acids that have been estimated with an accuracy or score    that exceeds a certain value is less than the certain specified    number, a peak with the largest m/z value is automatically selected    as a parent ion from those peaks containing amino acids whose    accuracy or score does not satisfy the certain value.-   (96) If the mass number of a single amino acid estimated from the    mass peak interval in the mass spectrum data is substantially    identical to the sum of the mass numbers of two or more, other kinds    of amino acids when they are linked, the MS^(n+1) analysis is    automatically conducted or the MS^(n) analysis is automatically    conducted again using a peak that contains that single amino acid.-   (97) If, as a result of the analysis of the mass peak interval of    the mass spectrum data, there is the possibility that an estimated    amino acid has a modifying structure such as phosphorylation, the    MS^(n+1) analysis is automatically conducted or the MS^(n) analysis    is automatically conducted again using a peak that contains that    amino acid.-   (98) In the analysis that is conducted on result of the n-th stage    mass spectroscopy (MS^(n)), namely the mass spectrum data    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio of an ion, one or more mass peaks that are    estimated to be derived from a single structural unit, such as a    dehydration peak derived from a peak in which a structural unit such    as an amino acid is detached, or a de-NH³ peak, are processed as a    group of peaks of the same kind, and then the number of the groups    of peaks of the same kind is calculated.-   (99) If the number of the groups of peaks of the same kind exceeds a    certain number designated by the user, for example, the next ion    measurement is performed or the measurement is terminated, and if    the number is less than the certain number, the MS^(n+1) is    conducted or the MS^(n) analysis is conducted again.-   (100) When conducting the MS^(n+1) or repeating the MS^(n) analysis    in the event that the number of the groups of peaks of the same kind    is less than the certain number specified by the user, for example,    a parent ion is automatically selected from groups of peaks with    large m/z values where the interval between one peak group and    another is maximum.-   (101) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, if the substance as a measurement object is a sugar    chain, a relevant monosaccharide or the structure of several    monosaccharides linked together is estimated from the mass peak    interval in the mass spectrum data.-   (102) When estimating the relevant monosaccharide or the structure    of several monosaccharides linked together from the mass peak    interval in the mass spectrum data, the number of monosaccharides or    structures consisting of several monosaccharides linked together    that have been estimated with an accuracy or score exceeding a    certain value is derived.-   (103) If the number of the monosaccharides that have been estimated    with an accuracy or score of more than a certain value is not less    than a certain number designated by the user, for example, the next    MS¹ analysis measurement is conducted or terminated, and if the    number is less than the certain designated number, the MS^(n+1)    analysis in which one of the ion species detected in the MS^(n) data    (n≧2) is selected, dissociated and subjected to mass spectroscopy is    conducted, or if an ion species with a substantially identical mass    number and a different valence from the mass number of the parent    ion in the MS^(n) analysis, that ion species is selected and    dissociated as the parent ion and the MS^(n) analysis is    automatically conducted again.-   (104) When conducting the MS^(n+1) analysis or repeating the MS^(n)    analysis in the event that the number of the saccharides that have    been estimated with an accuracy or score exceeding a certain value    is less than a certain number designated by the user, for example, a    peak with the largest m/z value is automatically selected as a    parent ion from the peaks containing monosaccharides whose accuracy    or score does not satisfy the certain value.-   (105) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, an isotope peak is determined within a specific time    period and eliminated from the MS^(n) (n≧2) spectrum data on which    the analysis is performed.-   (106) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, an isotope peak and the valence of each ion are    determined within a specific time period, wherein the analysis is    conducted on the spectrum data or a peak list from which the isotope    peak is eliminated and in which the ions are converted into    monovalent ions.-   (107) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, an isotope peak and the valence of ions are determined.-   (108) The next MS^(n) analysis refers to the MS^(n+1) (n≧2) analysis    in which one of the ion species detected in the MS^(n) data (n≧2) is    selected, dissociated and subjected to mass spectroscopy.-   (109) In the case where, as the next MS^(n) analysis content, an ion    species with substantially identical mass number and a different    valence from the parent ion in the MS^(n) analysis has been    detected, the MS¹ analysis (n≧2) is conducted using the ion species    as the parent ion.-   (110) An intensity distribution in mass spectrum data is analyzed on    the basis of the ease with which individual amino acids can be    dissociated from one another, or a database of the intensity    distribution.-   (111) When conducting the MS^(n+1) analysis or repeating the MS^(n)    analysis in the event that the number of the amino acids that have    been estimated with an accuracy or score exceeding a certain value    is less than a designated certain number, a y ion is preferentially    selected as the parent ion.-   (112) When conducting the MS^(n+1) analysis or repeating the MS^(n)    analysis in the event that the number of the amino acids that have    been estimated with an accuracy or score exceeding a certain value    is less than a designated certain number, a bivalent ion is    preferentially selected as the parent ion.-   (113) In the even that a sequence is contained in the amino acid    sequences estimated from the mass peak interval in the mass spectrum    data in which dissociation is not easily caused, the MS^(n+1)    analysis is conducted or the MS^(n) analysis is repeated.-   (114) In the even that a designated sequence is contained in the    amino acid sequences estimated from the mass peak interval in the    mass spectrum data, the MS^(n+1) analysis is conducted or the MS^(n)    analysis is repeated.-   (115) A de novo peptide sequence method is used as the method of    estimating the structural unit forming the parent ion within a    specific time period.-   (116) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, peaks with an intensity less than a threshold value    that is designated by the user or automatically set are eliminated,    and then the number of remaining peaks is derived, wherein the next    analysis content is determined based on the number of the mass    peaks.-   (117) In the next analysis content, the next MS¹ analysis    measurement is conducted or the measurement is terminated if the    number of the mass peaks is not less than a certain number    designated by the user, for example, and if the number of the mass    peaks is less than the designated number, the MS^(n+1) analysis is    conducted in which one of the ion species detected in the MS^(n)    data (n≧2) is selected, dissociated and subjected to mass    spectroscopy, or, if an ion species with substantially identical    mass number and a different valence from the parent ion in the    MS^(n) analysis has been detected in the MS^(n−1) data, the ion    species is selected and dissociated as the parent ion and the MS^(n)    analysis is automatically repeated.-   (118) In the analysis of the result of the n-th stage mass    spectroscopy (MS^(n)), namely the mass spectrum measurement result    represented in terms of a peak of measurement intensity against the    mass-to-charge ratio m/z of an ion, within the real time of    measurement, a database search is conducted, in which database    peptide sequences or the mass numbers thereof are stored upon    enzymatic digestion of protein sequences.-   (119) Based on mass spectrum measurement data, the peptide sequences    in the database are further divided into partial sequences, the    database in which the mass numbers of the peptide sequences are    stored is searched, and the MS^(n+1) analysis is conducted or the    MS^(n) analysis is repeated only for an ion for which no peptide has    been identified.    (120) When automatically conducting the MS^(n+1) analysis or    repeating the MS^(n) analysis in the event that the number of the    amino acids that have been decoded is less than a certain designated    number, if the valence of the parent ion in the MS^(n) mass spectrum    data that have been decoded is one, and if an ion species has been    detected in the MS^(n−1) data that has substantially identical mass    number and a different valence (two or more) from the parent ion in    the MS^(n) analysis, the ion species is selected and dissociated as    the parent ion and the MS^(n) analysis is repeated.    (121) When automatically conducting the MS^(n+1) analysis or    repeating the MS^(n) analysis in the event that the number of the    amino acids that have been decoded is less than a certain designated    number, if the valence of the parent ion in the MS^(n) mass spectrum    data that have been decoded is two or more, the MS^(n+1) analysis is    conducted.

Thus, in accordance with the present invention, automatic determinationsystems are provided in which, when conducting mass spectroscopy(MS^(n)) involving dissociation in multiple stages, the informationcontained in the MS^(n) spectrum is effectively utilized in each stageof MS^(n), and in which analysis flows for the determination of the nextanalysis content and for the selection of a parent ion for the MS^(n+1)analysis, for example, can be optimized within the real time ofmeasurement and with high efficiency and high accuracy. Thus, thesystems make it possible to conduct tandem mass spectroscopy on a targetof concern to the user.

Further, in accordance with the present invention, ions that are not theobjects of analysis can be eliminated prior to a primary massspectroscopy, so that the detection of an ion as the analysis object canbe facilitated during the primary mass spectroscopy. Accordingly, thetandem mass spectroscopy of a target substance (analysis object ion) canbe conducted on even a sample with much impurity components.

Further, in accordance with the present invention, particularly in thecase of a mass spectrometer using an ion trap, the trapping of ions thatare not the objects of analysis is made more difficult, so that theinfluence of space-charge effect in the ion trap can be reduced. Thus, atarget substance (analysis object ion) can be subjected to tandem massspectroscopy with high sensitivity.

1. A mass spectroscopy system comprising: ionization means for ionizinga substance as an object of measurement for a mass spectrometer; andmeans for selecting an ion species with a specific mass-to-charge ratiom/2 from ions produced by said ionization means and dissociating thesame, wherein the selection, dissociation and measurement of the ionspecies as the measurement object are repeated in a plurality of stages,said mass spectroscopy system further comprising: mass spectroscopy dataacquisition means for performing the selection and dissociation of anion species n−1 times (n≧1, where n is an integer) and acquiring a peakof measurement intensity against the mass-to-charge ratio of the ionthat has been selected and dissociated; correspondence determinationmeans for comparing the peak of measurement intensity against themass-to-charge ratio of the ion that is obtained by the massspectroscopy data acquisition means with the characteristics data of acertain ion species in order to determine the possibility ofcorrespondence of the ion that has been selected and dissociated to thecertain ion species; and next-analysis content determination means fordetermining the analysis content in an n-th stage mass spectroscopybased on the result of determination by said correspondencedetermination means.
 2. The mass spectroscopy system according to claim1, wherein an ion peak corresponding to an ion that has been determinedto correspond to the predetermined ion species is avoided from beingselected as the target for the selection and dissociation in the nextanalysis,
 3. The mass spectroscopy system according to claim 1, whereinin the next analysis content in the n-th stage mass spectroscopydetermined by said next analysis content determination means, an ionspecies with a certain m/z value is selected from the n-th stage massspectrum, an n-th dissociation is conducted, and an n+1-th stake massspectroscopy measurement is conducted.
 4. The mass spectroscopy systemaccording to claim 1, wherein in the next analysis content in the n-thstage mass spectroscopy determined by the next analysis contentdetermination means, an ion peak is selected from the n−1-th stage massspectrum measurement result that has a different m/z value from that ofthe ion peak with the certain m/z value that has been selected in then−1-th stage mass spectrum when the n-th stage mass spectrum measurementresult was obtained, the thus selected ion peak is dissociated, and then-th stage mass spectroscopy is repeated.
 5. The mass spectroscopysystem according to claim 1, wherein said correspondence determinationmeans determines correspondence within a certain tolerance or range. 6.A mass spectroscopy system according to claim 1, wherein, in the casewhere there is a mixture of a sample that is labeled by an isotope and asample that is not labeled by an isotope in a preprocessing stage ofmass spectroscopy, the characteristics data of the predetermined ionspecies is the characteristics data of an ion derived from the samplelabeled by an isotope.
 7. A mass spectroscopy system according to claim1, wherein said characteristics data include the mass number, valence,mass-to-charge ratio m/z value, and detection intensity of an ionspecies, the retention time of liquid chromatography (LC) or gaschromatography (GC), the solvent for LC or GC or its mobile-phase ratio,the flow volume or gradient of LC or GC, a sample number of the samplethat has been divided during the ion exchange in the one-dimensional ECin cases where a two-dimensional LC is used, the spot position, numberor coordinates on a sample plate in cases where a MALDI ion source isemployed, the content of measures to be taken for each of the ionspecies that corresponded to the stored characteristics data, analysisconditions including the date/time of measurement, a column number ofthe LC or GC used, an order n of the tandem mass spectroscopy MS^(n),and the operating condition of the mass spectrometer, and informationabout the inferred structure of an ion species.
 8. The mass spectroscopysystem according to claim 7, wherein the content of measures to be takenis in accordance with a user specification.
 9. The mass spectroscopysystem according to claim 7, wherein the user specification includes atleast one of whether or not a particular ion species should be excludedfrom the target ion species for the next MS^(n) (n≧1) analysis, whetheror not a particular ion species should be selected as the target ionspecies for the next MS^(n) (n≧1) analysis, and whether or not theparticular ion species should be removed upon or prior to the injectionof an ion sample into the mass spectroscopy system.
 10. The massspectroscopy system according to claim 7 ,wherein the ion species is anamino acid sequence, as in cases involving a protein or peptide sample.11. The mass spectroscopy system according to claim 7, furthercomprising a function for automatically correcting of calibrating theretention time of actually measured data concerning liquidchromatography (LC) or gas chromatography (GC) on the basis of acomparison between an actually measured retention time of a designatedreference substance that is already stored in a database provided in thesystem.
 12. The mass spectroscopy system according to claim 7, furthercomprising a function whereby; the mass number of an ion species isautomatically is automatically corrected or calibrated to be the massnumber without isotope peak upon deriving of the mass number, andwhereby; the mass-to-charge ratio m/z value of the ion species isautomatically corrected of calibrated if the m/z value fluctuates astime elapses from the start of measurement, on the basis of a comparisonbetween an actually measured m/z value of at least one referencesubstance with a known m/z value that is contained in the sample, andthe known m/z value, wherein said actually measured m/z value is thoseof the reference substances with different retention times of LC or GCin the case where there is more than one reference substance.
 13. A massspectroscopy system comprising: ionization means for ionizing asubstance as an object of measurement for a mass spectrometer; and massspectroscopy means for selecting an ion species with a specificmass-to-charge ratio m/z from ions produced by said ionization means anddissociating the same, and for repeating the selection, dissociation andmeasurement of the ion species as the measurement object in a pluralityof stages, said mass spectroscopy system further comprising: massspectroscopy data acquisition means for acquiring information about apeak of measurement intensity against the mass-to-charge ratio of ann-th stage ion obtained by said mass spectroscopy means; isotope peakdetermination means for determining an isotope peak based on ion massspectroscopy data acquired by said mass spectroscopy data acquisitionmeans; and next analysis content determination means for determining thenext n-th stage analysis content based on the isotope peak determined bysaid isotope peak determination means.
 14. A mass spectroscopy systemcomprising: an ion source for ionizing a sample; ionization means forionizing a substance as an object oil measurement for a massspectrometer; and means for selecting an ion species with a specificmass-to-charge ratio m/z from ions produced by said ionization means anddissociating the same, wherein the selection, dissociation andmeasurement of the ion species as the measurement object are repeated ina plurality of stages, said mass spectroscopy system further comprising:a mass spectroscopy data acquisition means for performing the selectionand dissociation of an ion species n−1 times (n≧1, where n is aninteger) and acquiring a peak of measurement intensity against themass-to-charge ratio of the ion that has been selected and dissociatedcorrespondence determination means for comparing the peak of measurementintensity against the mass-to-charge ratio of the ion that is obtainedby the mass spectroscopy data acquisition means with the characteristicsdata of a certain ion species in order to determine the possibility ofcorrespondence of the ion that has been selected and dissociated to thecertain ion species; next-analysis content determination means fordetermining the analysis content in an n-th stage mass spectroscopybased on the result of determination by said correspondencedetermination means; an RF power supply means for applying an RF voltagefor eliminating ions that are not analysis objects prior to a primarymass spectroscopy; and a control portion means for outputting ainstruction for the elimination of the non-analysis object ions to saidRF power supply.
 15. The mass spectroscopy system according to claim 14,further comprising a display portion for allowing the designation ofsaid analysis object ion and said non-analysis object ions.
 16. The massspectroscopy system according to claim 14, comprising a trap portion fortrapping said ion, wherein an RF voltage is applied from said RF powersupply to said trap portion in order to eliminate said non-analysis ionsprior to said primary mass spectroscopy.
 17. The mass spectroscopysystem according to claim 14, further comprising a first database forsearching for the data sequence of said analysis object candidatesubstance, wherein said control portion outputs an instruction forperforming mass spectroscopy on a dissociated ion produced bydissociating a substance retrieved concerning the data sequence of saidanalysis object candidate substance, and wherein said mass spectroscopydata acquisition means conducts mass spectroscopy on an ion derived fromthe retrieved selected ion species in response to the instruction fromsaid control portion.
 18. The mass spectroscopy system according toclaim 17, wherein said first database communicates with an externaldatabase so that a file concerning the data sequence of said analysisobject candidate substance can be updated.
 19. A mass spectrummeasurement employing an apparatus comprising an ion source, a massspectroscopy portion, and an RF power supply, said method comprising:ionizing a sample using said ion source, as an object of measurement fora mass spectrometer; selectively eliminating non-analysis object ionsfrom the ions obtained by the ionization, using said RF power supply;selecting an ion species with a specific mass-to-charge ratio m/z fromsaid ions produced from said sample and dissociating the same, whereinthe selection, dissociation and measurement of the ion species as themeasurement object are repeated in a plurality of stages, said methodoccurring within said mass spectroscopy portion and further comprising:selecting and dissociating an ion species n−1 times (n≧1, where n is aninteger) and acquiring a peak of measurement intensity against themass-to-charge ratio of the ion that has been selected and dissociated;comparing the peak of measurement intensity against the mass-to chargeratio of the ion that is obtained by the mass spectroscopy dataacquisition means with the characteristics data of a certain ion speciesin order to determine the possibility of correspondence of the ion thathas been selected and dissociated to the certain ion species;determining the analysis content in an n-th stage mass spectroscopybased on the result determination by said correspondence determinationmeans.
 20. The mass spectrum measurement according to claim 19, wherein,using said apparatus further comprising a first database in which a datasequence of an analysis object candidate substance is recorded and acontrol portion, from the data concerning a primary mass spectroscopythat is entered from said mass spectroscopy portion, data thatcorresponds to the data contained in said first database is retrieved,and an ion concerning the corresponding data is selectively dissociated,and a resultant dissociated ion is subjected to a secondary massspectroscopy in said mass spectroscopy portion.
 21. The mass spectrummeasurement according to claim 20, wherein, in said first database, thedata about said analysis object candidate substance is stored in termsof a data structure for each of the species including the human speciesand other species.
 22. The mass spectrum measurement according to claim20, wherein said RF power supply applies an RF voltage in order toeliminate an ion that does not correspond to the data in said firstdatabase prior to said primary mass spectroscopy, and wherein saidcontrol portion outputs instructions for the elimination of said ionthat does not correspond, said dissociation after said primary massspectroscopy, and the carrying out of said secondary mass spectroscopy.23. The mass spectrum measurement according to claim 22, wherein in saidfirst database, the data about an analysis object candidate substance isstored in terms of a data structure for each of the species includingthe human species and other species.
 24. The mass spectrum measurementaccording to 20, wherein, using said apparatus that further comprises asecond database in which data about non-analysis object candidatesubstance is recorded, a non-analysis object ion that corresponds to thedata contained in said secondary database is eliminated prior to primarymass spectroscopy so that an analysis object ion can be selectivelysubjected to said primary mass spectroscopy.
 25. The mass spectrummeasurement according to claim 24, wherein said RF power supply appliesan RF voltage in order to eliminate a non-analysis object ion thatcorresponds to the data in said second database prior to said primarymass spectroscopy, and wherein said control portion outputs instructionsfor the elimination of said non-analysis object ion, the dissociation ofsaid analysis object ion following said primary mass spectroscopy, andthe carrying out of said secondary mass spectroscopy.
 26. The massspectrum measurement according to claim 25, wherein an internal standardsubstance is added to a sample comprising said ion, and the analysisobject substance is quantitatively determined.
 27. A mass spectroscopyapparatus comprising: an ion source for ionizing a sample; a firstdatabase in which a data sequence of an analysis object candidatesubstance is recorded; a control portion for issuing an instruction forselecting an analysis object ion that corresponds to the data in saidfirst database; and a mass spectroscopy portion for performing a primarymass spectroscopy on an ion obtained by ionizing said sample andsubjecting a dissociated ion produced by the dissociation of theselected analysis object ion to a secondary mass spectroscopy.
 28. Themass spectroscopy apparatus according to claim 27, further comprising anRF power supply, wherein said RF power supply applies an RF voltage inorder to eliminate an ion that does not correspond to the data in saidfirst database prior to said primary mass spectroscopy, and wherein saidcontrol portion comprises means for carrying out the elimination of theion that does not correspond, the dissociation of said analysis objection following said primary mass spectroscopy, and said secondary massspectroscopy.
 29. The mass spectroscopy apparatus according to claim 28,further comprising an RF power supply, wherein said RF power supplyapplies an RF voltage in order to eliminate a non-analysis object ionthat corresponds to the data in said second database prior to saidprimary mass spectroscopy, and wherein said control portion comprisesmeans for carrying out the elimination of said non-analysis object ion,the dissociation of said analysis object ion following said primary massspectroscopy, and said secondary mass spectroscopy.